Here is the big commit, removing all PVM support, removing all autoto…

…ols, enabling a static build system with Makefiles, always using pthreads, and adding a default suffix of '2' to all programs and manual pages.
MichiganTech · Apr 10, 2018 · 4a9327d · 4a9327d
1 parent dd8f71f
commit 4a9327d
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diff --git a/Makefile b/Makefile
@@ -19,15 +19,15 @@ CC     = gcc
 # package will install. There must be a man page for each one of them
 # in the appropriate places (documentation/man for HMMER)
 #
-PROGS = binaries/hmmalign\
-	binaries/hmmbuild\
-	binaries/hmmcalibrate\
-	binaries/hmmconvert\
-	binaries/hmmemit\
-	binaries/hmmfetch\
-	binaries/hmmindex\
-	binaries/hmmpfam\
-	binaries/hmmsearch
+PROGS = hmmalign\
+        hmmbuild\
+        hmmcalibrate\
+        hmmconvert\
+        hmmemit\
+        hmmfetch\
+        hmmindex\
+        hmmpfam\
+        hmmsearch
 
 HMMER2_LIBS = libsquid.a \
               libhmmer.a
@@ -58,19 +58,23 @@ src/libhmmer.a:
 #          Prefix those paths with ${DESTDIR} (rarely used, usually null;
 #          may be set on a make command line when building contrib RPMs).
 install:
-	cd src ; install -D -t  ${DESTDIR}/$(BINDIR)/ $(PROGS)$(PROGSUFFIX)
-	for file in hmmer $(PROGS); do\
+	mkdir -p ${DESTDIR}/$(BINDIR)/
+
+	for file in $(PROGS) ; do\
+		cp src/$$file "${DESTDIR}/$(BINDIR)/$$file""$(PROGSUFFIX)" ;\
+	done
+	for file in hmmer2 $(ls documentation/man/); do\
 	   install -D documentation/man/$$file.man ${DESTDIR}/$(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\
 	done
 
 # Reverses the steps of "make install".  However, this should be handled
 # managed by a package management system like apt, rpm, pacman, or similar.
 uninstall:
 	for file in $(PROGS) ; do\
-	   rm ${BINDIR}/$$file;\
+	   rm "${BINDIR}/$$file""$(PROGSUFFIX)";\
 	done
-	for file in hmmer $(PROGS); do\
-	   rm $(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\
+	for file in hmmer2 $(ls documentation/man/); do\
+	   rm -f $(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\
 	done
 
 # after building, prep the whole directory for a binary distribution: symlink

diff --git a/Release-Notes/RELEASE-2.5j b/Release-Notes/RELEASE-2.5j
@@ -0,0 +1,14 @@
+HMMER 2.5j release notes
+Mon Apr 9 23:05:53 2018
+________________________________________________________________
+
+2.5j is a touch-up release.  There are no additional features, but a
+few stability enhancements, simplifications, and even feature removals.
+These changes are to allow co-installation with Hmmer3 and the coming
+Hmmer4.  The autotools build system and Parallel Virtual Machine
+support have been removed, as well as posix threads will now
+unconditionally be built.  This is not intended for further development
+as it was abandoned for a good reason.
+
+- Josh Marshall
+- Michigan Technological University
diff --git a/src/alphabet.c b/src/alphabet.c
@@ -1,10 +1,16 @@
 /************************************************************
- * @LICENSE@
+ * HMMER - Biological sequence analysis with profile HMMs
+ * Copyright (C) 1992-2006 HHMI Janelia Farm
+ * All Rights Reserved
+ * 
+ *     This source code is distributed under the terms of the
+ *     GNU General Public License. See the files COPYING and LICENSE
+ *     for details.
  ************************************************************/
 
 /* alphabet.c
  * Configuration of the global symbol alphabet information.
- * CVS $Id$
+ * CVS $Id: alphabet.c 910 2003-10-02 16:39:41Z eddy $
  */
 
 #include "config.h"
@@ -13,9 +19,7 @@
 #include <stdlib.h>
 #include <string.h>
 #include <ctype.h>
-#ifdef HMMER_THREADS
 #include <pthread.h>
-#endif /* HMMER_THREADS */
 
 #include "structs.h"
 #include "funcs.h"
@@ -82,15 +86,13 @@ void
 SetAlphabet(int type)
 {
   int x;
-#ifdef HMMER_THREADS
   pthread_mutex_t  alphabet_lock; /* alphabet is global; must protect to be threadsafe */
   int              rtn;		  /* return code from pthreads */
 
   if ((rtn = pthread_mutex_init(&alphabet_lock, NULL)) != 0)
     Die("pthread_mutex_init FAILED; %s\n", strerror(rtn));
   if ((rtn = pthread_mutex_lock(&alphabet_lock)) != 0)
     Die("pthread_mutex_lock FAILED: %s\n", strerror(rtn));
-#endif
 
  /* Because the alphabet information is global, we must
   * be careful to make this a thread-safe function. The mutex
@@ -105,10 +107,8 @@ SetAlphabet(int type)
       if (type != Alphabet_type) 
 	Die("An alphabet type conflict occurred.\nYou probably mixed a DNA seq file with a protein model, or vice versa.");
 
-#ifdef HMMER_THREADS
       if ((rtn = pthread_mutex_unlock(&alphabet_lock)) != 0)
 	Die("pthread_mutex_unlock failure: %s\n", strerror(rtn));
-#endif
       return;
     }
 
@@ -159,10 +159,8 @@ SetAlphabet(int type)
   default: Die("No support for non-nucleic or protein alphabets");  
   }
 
-#ifdef HMMER_THREADS
   if ((rtn = pthread_mutex_unlock(&alphabet_lock)) != 0)
     Die("pthread_mutex_unlock failure: %s\n", strerror(rtn));
-#endif
 }
 
 /* Function: SymbolIndex()

diff --git a/src/config.h b/src/config.h
@@ -9,7 +9,7 @@
 #pragma once
 
 /*****************************************************************
- * 1. This first section consists of compile-time constants that control 
+ * 1. This first section consists of compile-time constants that control
  *    HMMER's computational behavior (memory and processor use).
  *    It can be edited and configured manually before compilation.
  *****************************************************************/
@@ -30,7 +30,7 @@
 
 
 /*****************************************************************
- * 2. The next section consists of compile-time constants that control 
+ * 2. The next section consists of compile-time constants that control
  *    empirically tuned HMMER default parameters.
  *    You can edit it, but you ought not to, unless you're trying to
  *    improve on our empirical data.
@@ -67,14 +67,14 @@
 
 /*****************************************************************
  * 4. The final section isn't human editable at all.
- *    It is configured automatically by the ./configure script. 
+ *    It is configured automatically by the ./configure script.
  *    DO NOT EDIT BELOW THIS LINE.
  *****************************************************************/
 
 /* Version info - set once for whole package in configure.ac
  */
 #define PACKAGE_NAME "HMMER"
-#define PACKAGE_VERSION "2.4i"
+#define PACKAGE_VERSION "2.5j"
 #define PACKAGE_DATE "December 2006"
 #define PACKAGE_COPYRIGHT "Copyright (C) 1992-2006 HHMI Janelia Farm"
 #define PACKAGE_LICENSE "Freely distributed under the GNU General Public License (GPL)"

diff --git a/src/core_algorithms.c b/src/core_algorithms.c
@@ -1,10 +1,16 @@
 /************************************************************
- * @LICENSE@
+ * HMMER - Biological sequence analysis with profile HMMs
+ * Copyright (C) 1992-2006 HHMI Janelia Farm
+ * All Rights Reserved
+ * 
+ *     This source code is distributed under the terms of the
+ *     GNU General Public License. See the files COPYING and LICENSE
+ *     for details.
  ************************************************************/
 
 /* core_algorithms.c
  * SRE, Mon Nov 11 15:58:52 1996
- * CVS $Id$
+ * CVS $Id: core_algorithms.c 977 2004-12-12 00:02:03Z eddy $
  * 
  * Simple and robust "research" implementations of Forward, Backward,
  * and Viterbi for Plan7. For optimized replacements for some of these functions,
@@ -684,7 +690,7 @@ P7ViterbiTrace(struct plan7_s *hmm, unsigned char *dsq, int N,
   int curralloc;		/* current allocated length of trace */
   int tpos;			/* position in trace */
   int i;			/* position in seq (1..N) */
-  int k;			/* position in model (1..M) */
+  int k = 0;			/* position in model (1..M) */
   int **xmx, **mmx, **imx, **dmx;
   int sc;			/* temp var for pre-emission score */
 
@@ -1180,6 +1186,7 @@ P7ParsingViterbi(unsigned char *dsq, int L, struct plan7_s *hmm, struct p7trace_
    *  - When we enter B, we record the i of the best previous E, or 0 if there
    *    isn't one, in btr.
    */
+  cur = 1;
   for (i = 1; i <= L; i++) {
     cur = i % 2;
     prv = !cur;
@@ -1343,8 +1350,8 @@ P7WeeViterbi(unsigned char *dsq, int L, struct plan7_s *hmm, struct p7trace_s **
   int          *endlist;        /* stack of end points on sequence to work on */
   int          *startlist;      /* stack of start points on sequence to work on */
   int          lpos;            /* position in endlist, startlist */
-  int          k1, k2, k3;	/* start, mid, end in model      */
-  char         t1, t2, t3;	/* start, mid, end in state type */
+  int          k1, k2 = 0, k3;	/* start, mid, end in model      */
+  char         t1, t2 = 0, t3;	/* start, mid, end in state type */
   int          s1, s2, s3;	/* start, mid, end in sequence   */
   float        sc;		/* score of segment optimal alignment */
   float        ret_sc;		/* optimal score over complete seq */
@@ -1371,6 +1378,8 @@ P7WeeViterbi(unsigned char *dsq, int L, struct plan7_s *hmm, struct p7trace_s **
   tassign[1]      = STS;	/* temporary boundary condition! will become N or M */
   tassign[L]      = STT;	/* temporary boundary condition! will become M or C */
 
+  t2 = k2 = 0;
+
   /* Recursive divide-and-conquer alignment.
    */
   while (lpos >= 0)
@@ -1604,11 +1613,10 @@ Plan7ESTViterbi(unsigned char *dsq, int L, struct plan7_s *hmm, struct dpmatrix_
     mmx[i][0] = imx[i][0] = dmx[i][0] = -INFTY;
 
 				/* crude calculation of lookup value for codon */
+    codon = 64;             /* ambiguous codon; punt */
     if (i > 2) {
       if (dsq[i-2] < 4 && dsq[i-1] < 4 && dsq[i] < 4)
 	codon = dsq[i-2] * 16 + dsq[i-1] * 4 + dsq[i];
-      else
-	codon = 64;		/* ambiguous codon; punt */
     }
 
     for (k = 1; k <= hmm->M; k++) {

diff --git a/src/debug.c b/src/debug.c
@@ -1,5 +1,11 @@
 /*****************************************************************
- * @LICENSE@
+ * HMMER - Biological sequence analysis with profile HMMs
+ * Copyright (C) 1992-2006 HHMI Janelia Farm
+ * All Rights Reserved
+ * 
+ *     This source code is distributed under the terms of the
+ *     GNU General Public License. See the files COPYING and LICENSE
+ *     for details.
  *****************************************************************/
 
 /* debug.c
@@ -8,7 +14,7 @@
  * Printing out or naming various useful things from HMMER
  * innards.
  * 
- * CVS $Id$
+ * CVS $Id: debug.c 910 2003-10-02 16:39:41Z eddy $
  */
 
 #include "config.h"

diff --git a/src/display.c b/src/display.c
@@ -1,6 +1,12 @@
 /************************************************************
  * Copyright (C) 1998 Ian Holmes
- * @LICENSE@
+ * HMMER - Biological sequence analysis with profile HMMs
+ * Copyright (C) 1992-2006 HHMI Janelia Farm
+ * All Rights Reserved
+ * 
+ *     This source code is distributed under the terms of the
+ *     GNU General Public License. See the files COPYING and LICENSE
+ *     for details.
  ************************************************************/
 
 /* display.c
@@ -10,7 +16,7 @@
  * 
  * Functions for displaying HMMer2.0 structures.
  *
- * CVS $Id$
+ * CVS $Id: display.c 910 2003-10-02 16:39:41Z eddy $
  */
 
 #include "config.h"

diff --git a/src/emit.c b/src/emit.c
@@ -1,10 +1,16 @@
 /************************************************************
- * @LICENSE@
+ * HMMER - Biological sequence analysis with profile HMMs
+ * Copyright (C) 1992-2006 HHMI Janelia Farm
+ * All Rights Reserved
+ * 
+ *     This source code is distributed under the terms of the
+ *     GNU General Public License. See the files COPYING and LICENSE
+ *     for details.
  ************************************************************/
 
 /* emit.c
  * SRE, Sun Mar  8 12:26:58 1998
- * CVS $Id$
+ * CVS $Id: emit.c 913 2003-10-04 18:26:49Z eddy $
  * 
  * Generation of sequences/traces from an HMM.
  */

diff --git a/src/emulation.c b/src/emulation.c
@@ -1,13 +1,19 @@
 /************************************************************
- * @LICENSE@
+ * HMMER - Biological sequence analysis with profile HMMs
+ * Copyright (C) 1992-2006 HHMI Janelia Farm
+ * All Rights Reserved
+ * 
+ *     This source code is distributed under the terms of the
+ *     GNU General Public License. See the files COPYING and LICENSE
+ *     for details.
  ************************************************************/
 
 /* emulation.c
  * SRE, Wed Jan 21 07:50:01 1998
  * 
  * Interfaces between HMMER and other software packages.
  * 
- * CVS $Id$
+ * CVS $Id: emulation.c 878 2003-04-14 16:00:17Z eddy $
  */
 
 #include "config.h"

diff --git a/src/evolution.c b/src/evolution.c
@@ -1,11 +1,17 @@
 /************************************************************
- * @LICENSE@
+ * HMMER - Biological sequence analysis with profile HMMs
+ * Copyright (C) 1992-2006 HHMI Janelia Farm
+ * All Rights Reserved
+ * 
+ *     This source code is distributed under the terms of the
+ *     GNU General Public License. See the files COPYING and LICENSE
+ *     for details.
  ************************************************************/
 
 /* evolution.c
  * Routines for phylogenetic "extrapolation" of profile HMMs.
  * 
- * CVS $Id$
+ * CVS $Id: evolution.c 992 2005-01-21 17:02:32Z eddy $
  * incept: SRE, Sun Oct 31 08:13:33 2004 [St. Louis]
  */
 

diff --git a/src/fast_algorithms.c b/src/fast_algorithms.c
@@ -1,10 +1,16 @@
 /************************************************************
- * @LICENSE@
+ * HMMER - Biological sequence analysis with profile HMMs
+ * Copyright (C) 1992-2006 HHMI Janelia Farm
+ * All Rights Reserved
+ * 
+ *     This source code is distributed under the terms of the
+ *     GNU General Public License. See the files COPYING and LICENSE
+ *     for details.
  ************************************************************/
 
 /* fast_algorithms.c
  * SRE, Sun Nov 10 08:54:48 2002 [AA 3080, Denver to StL]
- * CVS $Id$
+ * CVS $Id: fast_algorithms.c 998 2005-01-26 22:11:49Z eddy $
  * 
  * Optimized routines to replace slower implementations in core_algorithms.c.
  *