Wrapper for Clustal Omega.

[jabaws.git] / binaries / src / clustalo / src / clustal / muscle_tree.h

diff --git a/binaries/src/clustalo/src/clustal/muscle_tree.h b/binaries/src/clustalo/src/clustal/muscle_tree.h
new file mode 100644 (file)
index 0000000..ff8a782
--- /dev/null
+++ b/binaries/src/clustalo/src/clustal/muscle_tree.h
@@ -0,0 +1,173 @@
+/* This a mix of tree functions and data-structures from
+ * Bob Edgar's Muscle (version 3.7) ported to pure C.
+ *
+ * Used files: phy.cpp, tree.h, phytofile.cpp and phyfromclust.cpp
+ *
+ * Muscle's code is public domain and so is this code here.
+
+ * From http://www.drive5.com/muscle/license.htm:
+ * """
+ * MUSCLE is public domain software
+ *
+ * The MUSCLE software, including object and source code and
+ * documentation, is hereby donated to the public domain.
+ *
+ * Disclaimer of warranty
+ * THIS SOFTWARE IS PROVIDED "AS IS" WITHOUT WARRANTY OF ANY KIND,
+ * EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION IMPLIED
+ * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * """
+ *
+ */
+
+/*
+ *  RCS $Id: muscle_tree.h 230 2011-04-09 15:37:50Z andreas $
+ */
+
+
+#ifndef CLUSTALO_MUSCLE_CLUSTALO_TREE_H
+#define CLUSTALO_MUSCLE_CLUSTALO_TREE_H
+
+#include <stdio.h>
+#include "util.h"
+
+#ifndef uint
+/* limit use of uint (see coding_style_guideline.txt) */
+typedef unsigned int uint;
+#endif
+
+static const uint NULL_NEIGHBOR = UINT_MAX;
+
+/**
+ * @brief guide-tree structure
+ *     
+ * @note We kept the original variable names here, to make it easy to
+ * search through Muscle's source code.
+ * From phy.cpp:
+ *    Node has 0 to 3 neighbors:
+ *    0 neighbors: singleton root
+ *    1 neighbor:  leaf, neighbor is parent
+ *    2 neigbors:  non-singleton root
+ *    3 neighbors: internal node (other than root)
+ *    
+ *    Minimal rooted tree is single node.
+ *    Minimal unrooted tree is single edge.
+ *    Leaf node always has nulls in neighbors 2 and 3, neighbor 1 is parent.
+ *    When tree is rooted, neighbor 1=parent, 2=left, 3=right.
+ *
+ */
+typedef struct {
+    uint m_uNodeCount;/**< number of nodes */
+    uint m_uCacheCount;/**< reserved memory */
+    
+    uint *m_uNeighbor1;/**< parent node */
+    uint *m_uNeighbor2;/**< left node */
+    uint *m_uNeighbor3;/**< right node */
+    
+    /* do we have edge lengths info stored (m_dEdgeLength[123]) */
+    bool *m_bHasEdgeLength1;
+    bool *m_bHasEdgeLength2;
+    bool *m_bHasEdgeLength3;
+
+    double *m_dEdgeLength1;
+    double *m_dEdgeLength2;
+    double *m_dEdgeLength3;
+    
+#if USE_HEIGHT
+    /* unused in our version of the code. we might need it at some
+     * stage so keep it in here, but disable via USE_HEIGHT throughout
+     * the code */
+    double *m_dHeight;
+    bool *m_bHasHeight;
+#endif
+
+    /**
+     * leaf labels.
+     * index range: 0 -- (m_uNodeCount+1)/2
+     */
+    char **m_ptrName;
+    
+    /**
+     * node id.
+     * index range: 0 -- m_uNodeCount
+     */
+    uint *m_Ids;
+    
+    bool m_bRooted; /**< tree is rooted */
+    uint m_uRootNodeIndex;
+} tree_t;
+
+
+extern void
+MuscleTreeCreate(tree_t *tree, uint uLeafCount, uint uRoot, const uint *Left,
+           const uint  *Right, const float *LeftLength, const float* RightLength,
+           const uint *LeafIds, char **LeafNames);
+
+extern void
+MuscleTreeToFile(FILE *fp, tree_t *tree);
+
+extern int
+MuscleTreeFromFile(tree_t *tree, char *ftree);
+
+extern void
+FreeMuscleTree(tree_t *tree);
+
+extern void
+LogTree(tree_t *tree, FILE *fp);
+
+extern bool
+IsRooted(tree_t *tree);
+
+extern uint
+GetNodeCount(tree_t *tree);
+
+extern uint
+GetLeafCount(tree_t *tree);
+        
+extern uint
+FirstDepthFirstNode(tree_t *tree);
+
+extern uint
+NextDepthFirstNode(uint nodeindex, tree_t *tree);
+
+extern bool
+IsLeaf(uint nodeindex, tree_t *tree);
+
+extern void
+SetLeafId(tree_t *tree, uint uNodeIndex, uint uId);
+    
+extern uint
+GetLeafId(uint nodeindex, tree_t *tree);
+
+extern char *
+GetLeafName(unsigned uNodeIndex, tree_t *tree);
+
+extern uint
+GetLeft(uint nodeindex, tree_t *tree);
+
+extern uint
+GetRight(uint nodeindex, tree_t *tree);
+
+extern uint
+GetRootNodeIndex(tree_t *tree);
+
+extern bool
+IsRoot(uint uNodeIndex, tree_t *tree);
+
+extern uint
+GetParent(unsigned uNodeIndex, tree_t *tree);
+
+extern double
+GetEdgeLength(uint uNodeIndex1, uint uNodeIndex2, tree_t *tree);
+
+extern uint
+LeafIndexToNodeIndex(uint uLeafIndex, tree_t *prTree);
+
+extern void
+AppendTree(tree_t *prDstTree,
+          uint uDstTreeNodeIndex, tree_t *prSrcTree);
+
+extern void
+TreeValidate(tree_t *tree);
+
+#endif