Merge pull request #2 from mradamczyk/ma/fix-draw

fix draw

drawDecomposition.py

@@ -10,29 +10,34 @@ def dnaComplementarity(x):
             'T': 'A'
             }.get(x, x)
 
-def check(f, word, i, j, delta, positions):
+def check(f, word, i, j, delta, positions, mode):
     if delta < 0:
         return None
     if i > j:
         deletion, swap = False, False
         return [(word[l], any(p == l for p in positions), any(p == l+len(word) for p in positions))
                 for l in xrange(len(word))]
     end = None
+
     if word[i] == f(word[j]):
-        end = check(f, word, i+1, j-1, delta, positions)
-    if end is not None:
-        return end
-    end = check(f, word, i+1, j, delta-1, positions + [i])
+        end = check(f, word, i+1, j-1, delta, positions, mode)
     if end is not None:
         return end
-    end = check(f, word, i, j-1, delta-1, positions + [j])
-    if end is not None:
-        return end
-    end = check(f, word, i+1, j-1, delta-1, positions + [i+len(word), j+len(word)])
+
+    if mode == 'edit':
+        end = check(f, word, i+1, j, delta-1, positions + [i], mode)
+        if end is not None:
+            return end
+
+        end = check(f, word, i, j-1, delta-1, positions + [j], mode)
+        if end is not None:
+            return end
+
+    end = check(f, word, i+1, j-1, delta-1, positions + [i+len(word), j+len(word)], mode)
     return end
 
-def word2nodes(f, word, delta):
-    letters = check(f, word, 0, len(word)-1, delta, [])
+def word2nodes(f, word, delta, mode):
+    letters = check(f, word, 0, len(word)-1, delta, [], mode)
     nodes = [('#', False, [])]
     last = nodes[-1]
     for (let, deletion, swap) in letters:
@@ -44,14 +49,16 @@ def word2nodes(f, word, delta):
     nodes.append(('#', False, []))
     return nodes
 
-def decomposition2graph(f, decomposition, delta):
+def decomposition2graph(f, decomposition, delta, mode):
     g = nx.Graph()
     words = decomposition.split(' ')
     #words = ['a','b','c']
     cnt = 1
     g.add_node(0, label='#', pos=[0, 0], color="white")
     last_x, last_y = 0, 0
     for w in words:
+        if len(w) == 0:
+            continue
         if w[0] == '[':
             if len(w) == 2:
                 continue
@@ -61,8 +68,9 @@ def decomposition2graph(f, decomposition, delta):
             cnt += 1
             last_x += 1 + (int(len(w)/5))
         else:
-            nodes = word2nodes(f, w, delta)
+            nodes = word2nodes(f, w, delta, mode)
             k = len(nodes) / 2
+            odd = len(nodes) % 2
             temp = []
             last_x += 1
             for i in xrange(k):
@@ -96,10 +104,19 @@ def decomposition2graph(f, decomposition, delta):
                     last_x -= 1 if i == k-1 else (0 if i == 0 else -1)
                 last_y = initial_y + mx * 2 - (0 if i != 0 or deletions1 or deletions2 else 2)
 
-            last_x += 2
+            if odd == 0:
+                last_x += 2
+            else:
+                last_x +=1
+                last_y += 1 if last_y != 0 else 0
+                g.add_node(cnt, label=nodes[k][0], pos=[last_x, last_y], color='black')
+                g.add_edge(cnt-1, cnt, style='bold')
+                cnt += 1
+                last_y -= 1 if last_y != 1 else 0
+                last_x += 1
 
             for i in xrange(k):
-                (let2, swap2, deletions2) = nodes[i+k]
+                (let2, swap2, deletions2) = nodes[i+odd+k]
                 (r_id, r_y) = temp.pop()
 
                 if i == k-1 and len(nodes[-2][2]) >= len(nodes[0][2]):
@@ -147,23 +164,25 @@ def drawGraph(g, fileName):
     G.render(fileName + '.gv')
 
 def main(argv):
-    dna, delta, fileName = False,  0, 'decomposition'
+    dna, delta, fileName, mode = False,  0, 'decomposition', 'edit'
     try:
-        opts, args = getopt.getopt(argv,"dE:f:")
+        opts, args = getopt.getopt(argv,"dHE:f:")
     except getopt.GetoptError:
-        print ('drawDecomposition.py [-d] [-E N] [-f fileName]')
+        print ('drawDecomposition.py [-d] [-H] [-E N] [-f fileName]')
         sys.exit(2)
     for opt, arg in opts:
         if opt == '-d':
             dna = True
+        elif opt == '-H':
+            mode = 'hamming'
         elif opt == '-E':
             delta = int(arg)
         elif opt == '-f':
             fileName = arg
 
     sys.stdin.readline()
     decomp = sys.stdin.readline().strip()
-    g = decomposition2graph(dnaComplementarity if dna else (lambda x: x), decomp, delta)
+    g = decomposition2graph(dnaComplementarity if dna else (lambda x: x), decomp, delta, mode)
     drawGraph(g, fileName)
 
 if __name__ == "__main__":

examples/eertree-ex1.dot

@@ -0,0 +1,46 @@
+digraph G {
+    size="6,6" ;
+    splines=true ; 
+    0:sw -> bb:nw [label="  b  "] ;
+
+    -1 -> a [label="  a  "] ;
+    -1 -> b [label="  b  "] ;
+    -1 -> c [label="  c   "] ;
+
+    b -> cbc [label="  c  "] ;
+    c -> bcb [label="  b  "] ;
+    cbc -> bcbcb [label="  b  "] ; 
+    bcbcb -> bbcbcbb [label="  b  "] ;
+    bbcbcbb-> abbcbcbba [label="  a  "] ;
+
+    0 -> -1 [style="dashed", color="blue", constraint=false] ;
+    -1:ne -> -1:nw [style="dashed", color="blue", constraint=false] ;
+    a -> 0 [style="dashed", color="blue", constraint=false] ;
+    b -> 0 [style="dashed", color="blue", constraint=false] ; 
+    c -> 0 [style="dashed", color="blue", constraint=false] ;
+    bb -> b [style="dashed", color="blue", constraint=false] ;
+    bcb -> b [style="dashed", color="blue", constraint=false] ;
+    cbc -> c [style="dashed", color="blue", constraint=false] ; 
+    bcbcb -> bcb [style="dashed", color="blue", constraint=false] ;
+    bbcbcbb -> bb [style="dashed", color="blue", constraint=false] ;
+    abbcbcbba -> a [style="dashed", color="blue", constraint=false] ;
+
+    bb -> 0 [style="dotted", color="red", dir=forward] ;
+    bcbcb:nw -> b [style="dotted", color="red"] ;
+
+
+    -1 [ pos = "2,6!"] ;
+    0 [ pos = "0,6!"] ;
+    a [ pos = "1,5!"] ;
+    b [ pos = "2,5!"] ;
+    c [ pos = "3,5!"] ;
+    bb [ pos = "0,4!"] ;
+    cbc [ pos = "2,3!"] ;
+    bcb [ pos = "3,3!"] ;
+    bcbcb [ pos = "2,2!"] ;
+    bbcbcbb [ pos = "2,1!"] ;
+    abbcbcbba [ pos = "2,0!"] ;
+
+    sep=0.3 ; 
+    nodesep=0.3 ;
+}

examples/eertree-ex2.dot

@@ -0,0 +1,44 @@
+digraph G {
+    splines=true ; 
+
+    0 -> GC [label=" C "]
+    0 -> CG [label=" G "]
+    0 -> TA [label="   A     "]
+    GC -> CGCG [label=" G "]
+    CGCG -> ACGCGT [label=" T "]
+    TA -> GTAC [label=" C "]
+    TA -> CTAG [label=" G   "]
+    CTAG -> ACTAGT [label=" T "]
+
+
+    GC:ne -> 0 [style="dashed", color="blue", constraint=false] ;
+    CG:n -> 0 [style="dashed", color="blue", constraint=false] ;
+    TA:n -> 0 [style="dashed", color="blue", constraint=false] ; 
+    GTAC:n -> 0 [style="dashed", color="blue", constraint=false] ;
+    CTAG -> 0 [style="dashed", color="blue", constraint=false] ;
+    ACGCGT:ne -> 0 [style="dashed", color="blue", constraint=false] ;
+    ACTAGT -> 0 [style="dashed", color="blue", constraint=false] ; 
+    CGCG -> CG [style="dashed", color="blue", constraint=false] ;
+
+
+    0 -> -1 [style="dashed", color="blue", constraint=false] ;
+    -1:ne -> -1:nw [style="dashed", color="blue", constraint=false] ;
+
+    CGCG:nw -> 0 [style="dotted", color="red", constraint=false] ;
+
+
+    0 [ pos="1,4!" ];
+    -1 [ pos="2,4!" ];
+    CG [ pos="0,2!" ];
+    GC [ pos="1,2!" ];
+    TA [ pos="4,2!" ];
+    CGCG [ pos="1,1!" ];
+    GTAC [ pos="3,1!" ];
+    CTAG [ pos="5,1!" ];
+    ACGCGT [ pos="1,0!" ];
+    ACTAGT [ pos="4,0!" ];
+
+    sep=0.3 ; 
+    nodesep=0.3 ;
+
+}

gen_figures.sh

@@ -1,8 +1,11 @@
-./max_pal_decomp_gaps_errors.x -d -G 4 -E 3 -L 14 -H -p < examples/ab220944.in | python drawDecomposition.py -d -E 3 -f max-pal-ham
+./max_pal_decomp_gaps_errors.x -d -G 4 -E 3 -L 14 -H -p < examples/ab220944.in | python drawDecomposition.py -d -H -E 3 -f max-pal-ham
 ./max_pal_decomp_gaps_errors.x -d -G 4 -E 3 -L 14 -p < examples/ab220944.in | python drawDecomposition.py -d -E 3 -f max-pal-edit-1
 ./max_pal_decomp_gaps_errors.x -d -G 4 -E 4 -L 20 -p < examples/ab220944.in | python drawDecomposition.py -d -E 4 -f max-pal-edit-2
 
 ./max_pal_decomp_gaps_errors.x -d -L 5 -G 2 -E 2 -p < examples/ab286863.in | python drawDecomposition.py -d -E 2 -f not-maximal-max
 ./all_pal_decomp_gaps_errors.x -d -L 5 -G 2 -E 2 -p < examples/ab286863.in | python drawDecomposition.py -d -E 2 -f not-maximal-all
 
 python ./drawDecomposition.py -d -E 1 < examples/vis-ex.in -f vis-ex
+
+cat examples/eertree-ex2.dot |  neato -Tpdf > eertree-ex2.pdf
+cat examples/eertree-ex1.dot |  neato -Tpdf > eertree-ex1.pdf