bio-velvet_underground 0.0.1

data/ext/src/src/fib.h

@@ -0,0 +1,78 @@
+/*
+Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
+
+    This file is part of Velvet.
+
+    Velvet 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.
+
+    Velvet is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with Velvet; if not, write to the Free Software
+    Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
+
+*/
+/*-
+ * Copyright 1997, 1998-2003 John-Mark Gurney.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ *    notice, this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright
+ *    notice, this list of conditions and the following disclaimer in the
+ *    documentation and/or other materials provided with the distribution.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE AUTHOR AND CONTRIBUTORS ``AS IS'' AND
+ * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED.  IN NO EVENT SHALL THE AUTHOR OR CONTRIBUTORS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
+ * OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+ * LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+ * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ * SUCH DAMAGE.
+ *
+ *	$Id: fib.h,v 1.9 2007/04/24 12:16:41 zerbino Exp $
+ *
+ */
+
+#ifndef _FIB_H_
+#define _FIB_H_
+
+#include "globals.h"
+
+typedef Coordinate(*voidcmp) (void *, void *);
+
+/* functions for key heaps */
+FibHeap *fh_makekeyheap(void);
+FibHeapNode *fh_insertkey(FibHeap *, Coordinate, void *);
+Coordinate fh_minkey(FibHeap *);
+Coordinate fh_replacekey(FibHeap *, FibHeapNode *, Coordinate);
+void *fh_replacekeydata(FibHeap *, FibHeapNode *, Coordinate, void *);
+
+/* functions for void * heaps */
+FibHeap *fh_makeheap(void);
+voidcmp fh_setcmp(FibHeap *, voidcmp);
+void *fh_setneginf(FibHeap *, void *);
+FibHeapNode *fh_insert(FibHeap *, void *);
+
+/* shared functions */
+void *fh_extractmin(FibHeap *);
+void *fh_min(FibHeap *);
+void *fh_replacedata(FibHeapNode *, void *);
+void *fh_delete(FibHeap *, FibHeapNode *);
+void fh_deleteheap(FibHeap *);
+FibHeap *fh_union(FibHeap *, FibHeap *);
+
+#endif				/* _FIB_H_ */

data/ext/src/src/fibHeap.c

@@ -0,0 +1,79 @@
+/*
+Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
+
+    This file is part of Velvet.
+
+    Velvet 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.
+
+    Velvet is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with Velvet; if not, write to the Free Software
+    Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
+
+*/
+#include <stdlib.h>
+
+#include "fib.h"
+#include "utility.h"
+
+// Constructor
+// Memory allocated
+FibHeap *newFibHeap()
+{
+	FibHeap * heap = fh_makekeyheap();
+	if (heap == NULL)
+		exitErrorf(EXIT_FAILURE, true, "Can't allocate FibHeap");
+	
+	return heap;
+}
+
+// Add new node into heap with a key, and a pointer to the specified node
+FibHeapNode *insertNodeIntoHeap(FibHeap * heap, Coordinate key,
+				struct node_st * node)
+{
+	return fh_insertkey(heap, key, node);
+}
+
+// Returns smallest key in heap
+Coordinate minKeyOfHeap(FibHeap * heap)
+{
+	return fh_minkey(heap);
+}
+
+// Replaces the key for a given node
+Coordinate replaceKeyInHeap(FibHeap * heap, FibHeapNode * node,
+			    Coordinate newKey)
+{
+	return fh_replacekey(heap, node, newKey);
+}
+
+// Removes the node with the shortest key, then returns it.
+struct node_st *removeNextNodeFromHeap(FibHeap * heap)
+{
+	return (struct node_st *) fh_extractmin(heap);
+}
+
+// Destructor
+void destroyHeap(FibHeap * heap)
+{
+	fh_deleteheap(heap);
+}
+
+// Replace the node pointed to by a heap node
+void replaceValueInHeap(FibHeapNode * node, Node * newValue)
+{
+	fh_replacedata(node, newValue);
+}
+
+// Remove unwanted node
+void destroyNodeInHeap(FibHeapNode * node, FibHeap * heap)
+{
+	fh_delete(heap, node);
+}

data/ext/src/src/fibHeap.h

@@ -0,0 +1,41 @@
+/*
+Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
+
+    This file is part of Velvet.
+
+    Velvet 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.
+
+    Velvet is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with Velvet; if not, write to the Free Software
+    Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
+
+*/
+#ifndef _FIBHEAP_H_
+#define _FIBHEAP_H_
+
+FibHeap *newFibHeap();
+
+FibHeapNode *insertNodeIntoHeap(FibHeap * heap, Coordinate key,
+				Node * node);
+
+Coordinate minKeyOfHeap(FibHeap * heap);
+
+Coordinate replaceKeyInHeap(FibHeap * heap, FibHeapNode * node,
+			    Coordinate newKey);
+
+void replaceValueInHeap(FibHeapNode * node, Node * newValue);
+
+Node *removeNextNodeFromHeap(FibHeap * heap);
+
+void *destroyNodeInHeap(FibHeapNode * node, FibHeap * heap);
+
+void destroyHeap(FibHeap * heap);
+#endif

data/ext/src/src/fibpriv.h

@@ -0,0 +1,110 @@
+/*
+Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
+
+    This file is part of Velvet.
+
+    Velvet 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.
+
+    Velvet is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with Velvet; if not, write to the Free Software
+    Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
+
+*/
+/*-
+ * Copyright 1997, 1999-2003 John-Mark Gurney.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ *    notice, this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright
+ *    notice, this list of conditions and the following disclaimer in the
+ *    documentation and/or other materials provided with the distribution.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE AUTHOR AND CONTRIBUTORS ``AS IS'' AND
+ * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED.  IN NO EVENT SHALL THE AUTHOR OR CONTRIBUTORS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
+ * OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+ * LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+ * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ * SUCH DAMAGE.
+ *
+ *	$Id: fibpriv.h,v 1.10 2007/10/09 09:56:46 zerbino Exp $
+ *
+ */
+
+#ifndef _FIBPRIV_H_
+#define _FIBPRIV_H_
+
+#include "globals.h"
+
+/*
+ * specific node operations
+ */
+struct fibheap_el {
+	FibHeapNode *fhe_p;
+	FibHeapNode *fhe_child;
+	FibHeapNode *fhe_left;
+	FibHeapNode *fhe_right;
+	void *fhe_data;
+	Coordinate fhe_key;
+	int fhe_degree;
+	boolean fhe_mark;
+};
+
+static FibHeapNode *fhe_newelem(struct fibheap *);
+static void fhe_initelem(FibHeapNode *);
+static void fhe_insertafter(FibHeapNode * a, FibHeapNode * b);
+static inline void fhe_insertbefore(FibHeapNode * a, FibHeapNode * b);
+static FibHeapNode *fhe_remove(FibHeapNode * a);
+
+/*
+ * global heap operations
+ */
+struct fibheap {
+	Coordinate(*fh_cmp_fnct) (void *, void *);
+	RecycleBin *nodeMemory;
+	IDnum fh_n;
+	IDnum fh_Dl;
+	FibHeapNode **fh_cons;
+	FibHeapNode *fh_min;
+	FibHeapNode *fh_root;
+	void *fh_neginf;
+	boolean fh_keys;
+};
+
+static void fh_initheap(FibHeap *);
+static void fh_insertrootlist(FibHeap *, FibHeapNode *);
+static void fh_removerootlist(FibHeap *, FibHeapNode *);
+static void fh_consolidate(FibHeap *);
+static void fh_heaplink(FibHeap * h, FibHeapNode * y, FibHeapNode * x);
+static void fh_cut(FibHeap *, FibHeapNode *, FibHeapNode *);
+static void fh_cascading_cut(FibHeap *, FibHeapNode *);
+static FibHeapNode *fh_extractminel(FibHeap *);
+static void fh_checkcons(FibHeap * h);
+static void fh_destroyheap(FibHeap * h);
+static int fh_compare(FibHeap * h, FibHeapNode * a, FibHeapNode * b);
+static int fh_comparedata(FibHeap * h, Coordinate key,
+			  void *data, FibHeapNode * b);
+static void fh_insertel(FibHeap * h, FibHeapNode * x);
+
+/*
+ * general functions
+ */
+static inline IDnum ceillog2(IDnum a);
+
+#endif				/* _FIBPRIV_H_ */

data/ext/src/src/globals.h

@@ -0,0 +1,153 @@
+/*
+Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
+
+    This file is part of Velvet.
+
+    Velvet 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.
+
+    Velvet is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with Velvet; if not, write to the Free Software
+    Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
+
+*/
+#ifndef _GLOBALS_H_
+#define _GLOBALS_H_
+
+#ifndef NULL
+#define NULL 0
+#endif
+
+#ifndef true
+#define true 1
+#define false 0
+#endif
+
+#ifdef __GNUC__
+#define ATTRIBUTE_PACKED  __attribute__ ((packed))
+#else
+#define ATTRIBUTE_PACKED
+#endif
+
+#define VERSION_NUMBER 1
+#define RELEASE_NUMBER 2
+#define UPDATE_NUMBER 10
+
+#define MAXLINE 5000 
+
+#define LONG (2 * CATEGORIES)
+#define LONG_PAIRED (2 * CATEGORIES + 1)
+#define REFERENCE (2 * CATEGORIES + 2)
+
+/* NULL value for ArrayIdx */
+#define NULL_IDX 0
+
+#if defined(_WIN32) || defined(__WIN32__) || defined(WIN32)
+#define inline __inline
+extern struct tString_st;
+extern struct readSet_st;
+extern struct splayTable_st;
+extern struct annotation_st;
+extern struct roadmap_st;
+extern struct insertionMarker_st;
+extern struct arc_st;
+extern struct node_st;
+extern struct graph_st;
+extern struct passage_st;
+extern struct passageList_st;
+extern struct readStart_st;
+extern struct preArc_st;
+extern struct preNode_st;
+extern struct preGraph_st;
+extern struct fibheap;
+extern struct fibheap_el;
+extern struct dfibheap;
+extern struct dfibheap_el;
+extern struct kmerOccurence_st;
+extern struct kmerOccurenceTable_st;
+#endif
+
+// Namespace sizes
+#include <stdint.h>
+typedef int8_t boolean;
+typedef int8_t Nucleotide;
+typedef uint8_t Descriptor;
+#ifdef BIGASSEMBLY
+typedef int64_t IDnum;
+#else
+typedef int32_t IDnum;
+#endif
+typedef int64_t Coordinate;
+#ifdef LONGSEQUENCES
+typedef int32_t ShortLength;
+#else
+typedef int16_t ShortLength;
+#endif
+typedef double Time;
+typedef uint8_t Quality;
+typedef double Probability;
+typedef int8_t Category;
+#ifndef VBIGASSEMBLY
+typedef uint32_t ArrayIdx;
+#else
+typedef uint64_t ArrayIdx;
+#endif
+
+// Atomic word
+typedef struct kmer_st Kmer;
+typedef uint64_t KmerKey;
+
+// Just a sequence string, but with just two bits per character
+typedef struct tString_st TightString;
+
+// A simple container when reading files
+typedef struct readSet_st ReadSet;
+typedef struct sequenceReader_st SequenceReader;
+typedef struct sequencesReader_st SequencesReader;
+
+// Hash table structures
+typedef struct kmerOccurence_st KmerOccurence;
+typedef struct kmerOccurenceTable_st KmerOccurenceTable;
+typedef struct splayTable_st SplayTable;
+
+// Graph construction structures
+typedef struct annotationList_st AnnotationList;
+typedef struct annotation_st Annotation;
+typedef struct roadmap_st RoadMap;
+typedef struct roadMapArray_st RoadMapArray;
+typedef struct insertionMarker_st InsertionMarker;
+
+// Pre-Graph elements
+typedef struct preMarker_st PreMarker;
+typedef ArrayIdx PreArcI;
+typedef struct preNode_st PreNode;
+typedef struct preGraph_st PreGraph;
+
+// Graph elements
+typedef struct arc_st Arc;
+typedef struct node_st Node;
+typedef struct graph_st Graph;
+typedef struct shortReadMarker_st ShortReadMarker;
+typedef ArrayIdx PassageMarkerI;
+typedef struct passageList_st PassageMarkerList;
+typedef struct readStart_st ReadStart;
+typedef struct gapMarker_st GapMarker;
+
+// Fibonacci heaps used mainly in Tour Bus
+typedef struct fibheap FibHeap;
+typedef struct fibheap_el FibHeapNode;
+typedef struct dfibheap DFibHeap;
+typedef struct dfibheap_el DFibHeapNode;
+
+typedef struct nodeList_st NodeList;
+
+typedef struct mask_st Mask;
+
+#endif