[med-svn] r1712 - in trunk/packages: . tigr-glimmer tigr-glimmer/branches tigr-glimmer/branches/upstream tigr-glimmer/branches/upstream/current
charles-guest at alioth.debian.org
charles-guest at alioth.debian.org
Wed Apr 9 04:27:43 UTC 2008
Author: charles-guest
Date: 2008-04-09 04:27:42 +0000 (Wed, 09 Apr 2008)
New Revision: 1712
Added:
trunk/packages/tigr-glimmer/
trunk/packages/tigr-glimmer/branches/
trunk/packages/tigr-glimmer/branches/upstream/
trunk/packages/tigr-glimmer/branches/upstream/current/
trunk/packages/tigr-glimmer/branches/upstream/current/Makefile
trunk/packages/tigr-glimmer/branches/upstream/current/delcher.h
trunk/packages/tigr-glimmer/branches/upstream/current/run-glimmer2
Log:
[svn-inject] Installing original source of tigr-glimmer
Added: trunk/packages/tigr-glimmer/branches/upstream/current/Makefile
===================================================================
--- trunk/packages/tigr-glimmer/branches/upstream/current/Makefile (rev 0)
+++ trunk/packages/tigr-glimmer/branches/upstream/current/Makefile 2008-04-09 04:27:42 UTC (rev 1712)
@@ -0,0 +1,74 @@
+# -*- makefile -*-
+# just make headings for each thing and put the headings
+# on the line for ALL
+PROJECTDIR = .
+BINDIR = $(PROJECTDIR)
+
+CC = gcc
+CPPC = g++
+CFLAGS = -O3 -g -Wall
+LDFLAGS = -lm
+
+DEPEND_FILES = *.cc *.c *.h
+CLEANABLE_FILES = *.o *~
+
+ALL = adjust anomaly build-icm check codon-usage compare-lists \
+ extract generate get-len get-putative glimmer2 long-orfs
+
+.SUFFIXES: .cc .c
+
+.c.o:
+ $(CC) $(CFLAGS) -c $*.c -o $*.o
+
+.cc.o:
+ $(CPPC) $(CFLAGS) -c $*.cc -o $*.o
+
+all: $(ALL)
+
+adjust: adjust.o delcher.o
+ $(CPPC) -o $(BINDIR)/$@ adjust.o delcher.o $(LDFLAGS)
+
+anomaly: anomaly.o delcher.o gene.o
+ $(CPPC) -o $(BINDIR)/$@ anomaly.o delcher.o gene.o $(LDFLAGS)
+
+build-icm: build-icm.o misc.o
+ $(CC) -o $(BINDIR)/$@ build-icm.o misc.o $(LDFLAGS)
+
+check: check.o delcher.o
+ $(CPPC) -o $(BINDIR)/$@ check.o delcher.o $(LDFLAGS)
+
+codon-usage: codon-usage.o delcher.o gene.o
+ $(CPPC) -o $(BINDIR)/$@ codon-usage.o delcher.o gene.o $(LDFLAGS)
+
+compare-lists: compare-lists.o delcher.o
+ $(CPPC) -o $(BINDIR)/$@ compare-lists.o delcher.o $(LDFLAGS)
+
+extract: extract.o delcher.o
+ $(CPPC) -o $(BINDIR)/$@ extract.o delcher.o $(LDFLAGS)
+
+generate: generate.o delcher.o gene.o
+ $(CPPC) -o $(BINDIR)/$@ generate.o delcher.o gene.o $(LDFLAGS)
+
+get-len: get-len.o delcher.o
+ $(CPPC) -o $(BINDIR)/$@ get-len.o delcher.o $(LDFLAGS)
+
+get-putative: get-putative.o delcher.o
+ $(CPPC) -o $(BINDIR)/$@ get-putative.o delcher.o $(LDFLAGS)
+
+glimmer2: glimmer2.o delcher.o gene.o rnabin.o
+ $(CPPC) -o $(BINDIR)/$@ glimmer2.o delcher.o gene.o rnabin.o $(LDFLAGS)
+
+long-orfs: long-orfs.o delcher.o gene.o
+ $(CPPC) -o $(BINDIR)/$@ long-orfs.o delcher.o gene.o $(LDFLAGS)
+
+rnabin: rnabin.o delcher.o
+ $(CPPC) -o $(BINDIR)/$@ rnabin.o delcher.o $(LDFLAGS)
+
+depend:
+ makedepend $(DEPEND_FILES)
+
+clean:
+ /bin/rm -f $(CLEANABLE_FILES)
+
+# DO NOT DELETE THIS LINE -- make depend depends on it.
+
Added: trunk/packages/tigr-glimmer/branches/upstream/current/delcher.h
===================================================================
--- trunk/packages/tigr-glimmer/branches/upstream/current/delcher.h (rev 0)
+++ trunk/packages/tigr-glimmer/branches/upstream/current/delcher.h 2008-04-09 04:27:42 UTC (rev 1712)
@@ -0,0 +1,120 @@
+// A. L. Delcher
+//
+// File: ANNOTATION/Glimmer/delcher.h
+// Version: 2.03 3 Dec 2002
+//
+// Copyright (c) 2002 by Arthur Delcher, Steven Salzberg, Simon
+// Kasif, and Owen White. All rights reserved. Redistribution
+// is not permitted without the express written permission of
+// the authors.
+//
+// Common generic routines.
+//
+
+
+#ifndef __DELCHER_H_INCLUDED
+#define __DELCHER_H_INCLUDED
+
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <iostream.h>
+#include <iomanip.h>
+#include <fstream.h>
+#include <math.h>
+#include <string.h>
+#include <ctype.h>
+#include <limits.h>
+#include <float.h>
+#include <time.h>
+#include <assert.h>
+#include <errno.h>
+#include <unistd.h>
+
+
+#define TRUE 1
+#define FALSE 0
+#ifndef EXIT_FAILURE
+ #define EXIT_FAILURE -1
+#endif
+#ifndef EXIT_SUCCESS
+ #define EXIT_SUCCESS 0
+#endif
+
+
+const int FASTA_WIDTH = 60;
+ // Max number of characters to print on a FASTA data line
+
+
+const char * Commatize
+ (long int n);
+void Fasta_Print
+ (FILE * fp, char * s, char * hdr);
+void Fasta_Print_N
+ (FILE * fp, char * s, int n, char * hdr);
+FILE * File_Open
+ (const char *, const char *);
+double Percent
+ (double a, double b);
+void * Safe_calloc
+ (size_t N, size_t Len, size_t line_num = 0);
+void * Safe_malloc
+ (size_t Len, size_t line_num = 0);
+void * Safe_realloc
+ (void * Q, size_t Len, size_t line_num = 0);
+
+
+template <class DT>
+ DT Max (DT, DT);
+template <class DT>
+ DT Min (DT, DT);
+template <class DT>
+ void Swap (DT &, DT &);
+
+
+template <class DT>
+DT Max (DT A, DT B)
+
+// Return the larger of A and B .
+
+ {
+ if (A > B)
+ return A;
+ else
+ return B;
+ }
+
+
+
+template <class DT>
+DT Min (DT A, DT B)
+
+// Return the smaller of A and B .
+
+ {
+ if (A < B)
+ return A;
+ else
+ return B;
+ }
+
+
+
+template <class DT>
+void Swap (DT & A, DT & B)
+
+// Swap the values in A and B .
+
+ {
+ DT Save;
+
+ Save = A;
+ A = B;
+ B = Save;
+
+ return;
+ }
+
+
+
+#endif
Added: trunk/packages/tigr-glimmer/branches/upstream/current/run-glimmer2
===================================================================
--- trunk/packages/tigr-glimmer/branches/upstream/current/run-glimmer2 (rev 0)
+++ trunk/packages/tigr-glimmer/branches/upstream/current/run-glimmer2 2008-04-09 04:27:42 UTC (rev 1712)
@@ -0,0 +1,16 @@
+echo "run Glimmer2"
+clear
+echo "Genome is " $1
+echo "Find non-overlapping orfs in tmp.coord"
+rm -f tmp.coord
+long-orfs $1 | get-putative >tmp.coord
+echo "Extract training sequences to tmp.train"
+rm -f tmp.train
+extract $1 tmp.coord >tmp.train
+wc tmp.train
+echo "Build interpolated context model in tmp.model"
+rm -f tmp.model
+build-icm <tmp.train >tmp.model
+echo "Predict genes with Glimmer2 with coordinates in g2.coord"
+rm -f g2.coord
+glimmer2 $1 tmp.model | get-putative >g2.coord
Property changes on: trunk/packages/tigr-glimmer/branches/upstream/current/run-glimmer2
___________________________________________________________________
Name: svn:executable
+
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