little modifications

README.md

@@ -50,12 +50,60 @@ Launch _REQ_ without option to read the following documentation:
 
 The directory _example_ contains two files from the study of [Garcia-Hermoso et al. (2018)](https://doi.org/10.1128/mBio.00573-18):     
 * _matrix.d_: a distance matrix in PHYLIP square format estimated from 22 _Mucor circinelloides_ f. _circinelloides_ genomes,
-* _tree.t_: the associated Minimum Evolution phylogenetic tree in NEWICK format.
+* _tree.t_: the associated minimum-evolution phylogenetic tree in NEWICK format.
 
 The following command line writes into the file _tree.req.t_ the phylogenetic tree from _example/tree.t_ with the rate of elementary quartets at each internal branch estimated from the distance matrix _example/matrix.d_:
 ```bash
-REQ  example/matrix.d  example/tree.t  tree.req.t
+REQ  example/matrix.d  example/tree.t  tree.req.t  -v
 ```
+Because the option -v is set, the verbose mode will output the tree topology in NEWICK format, the list of leaf names, and, for each internal branch, the leaf quadripartition together with the rate of elementary quartets _Re_:
+```
+# (((((((17,18),16),((20,21),19)),(((4,((6,7),5)),(((2,3),1),0)),(8,9))),(10,11)),(12,13)),14,15);
+0: P07_621_SLS
+1: 1006PHL
+2: P08_701_BU2_PER
+3: P01_617_BU1_SLS
+4: P11_702_BU2_PER
+5: E01_615_SLS
+6: P04_601_BU1_SLS
+7: P04_559_BU1_SLS
+8: P05_600_BU1_SLS
+9: P05_598_BU1_SLS
+10: P04_603_BU1_SLS
+11: P04_602_BU1_SLS
+12: P06_032_BU1_SLS
+13: P06_023_BU1_SLS
+14: P02_783_BU1_SLS
+15: P12_579_STR
+16: P05_622_BU1_SLS
+17: P10_703_BU2_PER
+18: P09_704_BU2_PER
+19: P03_594_BU1_SLS
+20: P05_599_BU1_SLS
+21: P03_592_BU1_SLS
+[17][18][16][21,20,19,15,14,13,12,11,10,9,8,7,6,5,4,3,2,1,0] Re=1.000 (19/19)
+[18,17][16][19,21,20][15,14,13,12,11,10,9,8,7,6,5,4,3,2,1,0] Re=0.677 (65/96)
+[20][21][19][18,17,16,15,14,13,12,11,10,9,8,7,6,5,4,3,2,1,0] Re=0.474 (9/19)
+[21,20][19][16,18,17][15,14,13,12,11,10,9,8,7,6,5,4,3,2,1,0] Re=1.000 (96/96)
+[16,18,17][19,21,20][9,8,0,1,3,2,5,7,6,4][15,14,13,12,11,10] Re=0.856 (462/540)
+[6][7][5][21,20,19,18,17,16,15,14,13,12,11,10,9,8,4,3,2,1,0] Re=1.000 (19/19)
+[7,6][5][4][21,20,19,18,17,16,15,14,13,12,11,10,9,8,3,2,1,0] Re=0.944 (34/36)
+[4][5,7,6][0,1,3,2][21,20,19,18,17,16,15,14,13,12,11,10,9,8] Re=1.000 (168/168)
+[2][3][1][21,20,19,18,17,16,15,14,13,12,11,10,9,8,7,6,5,4,0] Re=1.000 (19/19)
+[3,2][1][0][21,20,19,18,17,16,15,14,13,12,11,10,9,8,7,6,5,4] Re=1.000 (36/36)
+[1,3,2][0][5,7,6,4][21,20,19,18,17,16,15,14,13,12,11,10,9,8] Re=1.000 (168/168)
+[5,7,6,4][0,1,3,2][9,8][21,20,19,18,17,16,15,14,13,12,11,10] Re=1.000 (384/384)
+[8][9][0,1,3,2,5,7,6,4][21,20,19,18,17,16,15,14,13,12,11,10] Re=1.000 (96/96)
+[0,1,3,2,5,7,6,4][9,8][19,21,20,16,18,17][15,14,13,12,11,10] Re=0.453 (261/576)
+[19,21,20,16,18,17][9,8,0,1,3,2,5,7,6,4][11,10][15,14,13,12] Re=0.488 (234/480)ù
+[10][11][9,8,0,1,3,2,5,7,6,4,19,21,20,16,18,17][15,14,13,12] Re=1.000 (64/64)
+[9,8,0,1,3,2,5,7,6,4,19,21,20,16,18,17][11,10][13,12][15,14] Re=0.594 (76/128)
+[12][13][11,10,9,8,0,1,3,2,5,7,6,4,19,21,20,16,18,17][15,14] Re=1.000 (36/36)
+[11,10,9,8,0,1,3,2,5,7,6,4,19,21,20,16,18,17][13,12][14][15] Re=0.500 (18/36)
+output tree written into tree.req.t
+```
+
+Of note, the output file _tree.req.t_ is available inside the directory _example_.
 
 ## References
 

example/tree.req.t

+(((((((P10_703_BU2_PER:0.000157849066,P09_704_BU2_PER:0.000209200934)1.000:0.000483122851,P05_622_BU1_SLS:0.001116966803)0.677:0.000018368078,((P05_599_BU1_SLS:0.000159586258,P03_592_BU1_SLS:0.000169023742)0.474:0.000015792325,P03_594_BU1_SLS:0.000128336869)1.000:0.000462006451)0.856:0.000081437521,(((P11_702_BU2_PER:0.000615002481,((P04_601_BU1_SLS:0.000117392803,P04_559_BU1_SLS:0.000164857197)1.000:0.000925936953,E01_615_SLS:0.000884566733)0.944:0.000161626490)1.000:0.008730158578,(((P08_701_BU2_PER:0.001390856250,P01_617_BU1_SLS:0.001385183750)1.000:0.001280565582,1006PHL:0.002499367591)1.000:0.011475862713,P07_621_SLS:0.014634622105)1.000:0.015451073655)1.000:0.008164485602,(P05_600_BU1_SLS:0.000172301484,P05_598_BU1_SLS:0.000210108516)1.000:0.000603348539)0.453:0.000010417106)0.488:0.000045431349,(P04_603_BU1_SLS:0.000255598014,P04_602_BU1_SLS:0.000179821986)1.000:0.000552675249)0.594:0.000029208891,(P06_032_BU1_SLS:0.000173131711,P06_023_BU1_SLS:0.000108148289)1.000:0.000554756800)0.500:0.000022656931,P02_783_BU1_SLS:0.000592772460,P12_579_STR:0.000673747540);
\ No newline at end of file

src/REQ.java

@@ -119,7 +119,7 @@ public class REQ {
 	//#                                                           sup    last
 	tr = tr.insert(0, '('); sup = apc(tr, tr.lastIndexOf(")")); tr = tr.insert(sup, ')'); //# NOTE: closing parenthesis at index 'sup' should not be considered for REQ calculations
 	last = tr.lastIndexOf(")"); 
-	if ( verbose ) { i = -1; while ( ++i < n ) System.out.println(i + ": " + lbl.get(i)); System.out.println("# " + tr.toString()); }
+	if ( verbose ) { i = -1; while ( ++i < n ) System.out.println(i + ": " + lbl.get(i)); /*System.out.println("# " + tr.toString());*/ }
 
 	ts = new TreeSet<Short>(); si = 0; --si; while ( ++si < n ) ts.add(new Short(si)); are = new ArrayList<Double>(); u = -1;
 	while ( (u=tr.indexOf(")", ++u)) != last ) {
@@ -129,7 +129,7 @@ public class REQ {
 	    if ( u == sup ) {
 		last = tro.lastIndexOf(")"); tr = tro.insert(last, ')'); v = apc(tr, apc(tr, last)); tr = tr.insert(++v, '(');
 		++last; //# NOTE: closing parenthesis at index 'last' should not be considered for REQ calculations
-		if ( verbose ) System.out.println("# " + tr.toString());
+		//if ( verbose ) System.out.println("# " + tr.toString());
 		sup = 0; --u; continue;
 	    }
 	    //# parsing every internal branch e at index u in order to obtain  lbl(STa) lbl(STb) | lbl(STc) lbl(T)-lbl(STa U STb U STc)  ########