// -------------- NewickToNexus ------------------
void NewickToNexus(phylo P)
{
//SWK - A Nexus wrapper takes a Newick file and makes it Mesquite readable
time_t rawtime;
int i;
char tmp[24];
time ( &rawtime );
strncpy(tmp , ctime(&rawtime), 24);
printf("#NEXUS\n[output from phylocom, written %s]\n\n", tmp );
printf("BEGIN TAXA;\n");
printf("TITLE Phylocom_Phylogeny_Taxa;\n"); // Needed for correct Mesquite grammar, but V1.1 busted! Will not read interior names correctly.
printf("\tDIMENSIONS NTAX=%d;\n\tTAXLABELS\n\t", P.termtaxa);
for (i = 0; i < P.nnodes; i++) {
if (P.noat[i] == 0) printf(" %s", P.taxon[i]);
}
printf(";\nEND;\n\n");
printf("BEGIN TREES;\n");
printf("\tTITLE Phylocom_Phylogenies;\n\tLINK Taxa = Phylocom_Phylogeny_Taxa;\n"); // Ditto!
//printf("\tTRANSLATE\n\t");
//for (i = 0; i < P.ntaxa; i++) printf(" %d %s;\n", i, P.taxon[P.t2n[i]]);
printf("\tTREE %s = ", P.phyname);
//Is there a way to exclude node labels? Might be useful... see fy2new.c
Fy2newRec(P);
printf("END;\n");
}
void Comnode(phylo t1, phylo t2)
{
int i, j, xnode, depth, common, matches1, matches2, p, q;
int matchcode = 0;
int t1md = 0;
int t2md = 0;
int *active_n;
int *matched1;
int *matched2;
int **comlist1; // contents: node number of a term taxon (use to lookup name)
// indexed by node, and then an index 0...
int *comlist1n; // the number of items in *comlist
int **comlist2; // contents: node number of a term taxon (use to lookup name)
// indexed by node, and then an index 0...
int *comlist2n; // the number of items in *comlist
char tmp[50];
phylo Out[1];
strcpy(t1.phyname, "Tree1");
// t1.arenotes = 1;
// t1.notes = cmatrix(0, t1.nnodes-1, 0, 49);
strcpy(t2.phyname, "Tree2");
// t2.arenotes = 1;
// t2.notes = cmatrix(0, t2.nnodes-1, 0, 49);
comlist1 = imatrix(0, t1.nnodes-1, 0, t1.termtaxa);
comlist1n = ivector(0, t1.nnodes-1);
comlist2 = imatrix(0, t2.nnodes-1, 0, t2.termtaxa);
comlist2n = ivector(0, t2.nnodes-1);
matched1 = ivector(0, t1.termtaxa-1);
matched2 = ivector(0, t2.termtaxa-1);
// printf("t1: nnodes: %d taxa1: %s\n", t1.nnodes, t1.taxalist[0]);
// printf("t2: nnodes: %d taxa1: %s\n", t2.nnodes, t2.taxalist[0]);
// make a full list of term taxa from each node:
// tree1:
for (i = 0; i < t1.nnodes; i++)
{
if (t1.depth[i] > t1md) t1md = t1.depth[i];
// need to clear the node names - they could cause confusion
// when bladjing, beacause the default names are the same for both
// trees
if (t1.noat[i] > 0) strcpy(t1.taxon[i], ".");
// these will get unmaned: see fy2new
}
active_n = ivector(0, t1.nnodes-1);
for (i = 0; i < t1.nnodes; i++)
{
active_n[i] = 1;
comlist1n[i] = 0;
for (depth = t1.depth[i]; depth <= t1md; depth++)
{
for (xnode = 0; xnode < t1.nnodes; xnode++)
{
if ( (t1.depth[xnode] == depth) && (active_n[xnode] == 1) )
{
// first we check to see if we have reached a tip
if (t1.noat[xnode] == 0)
{
// test to see that it is a common spp to tree 2
common = 0;
for (j = 0; j < t2.termtaxa; j++)
{
if (strcmp(t1.taxon[xnode], t2.taxalist[j]) == 0)\
common = 1;
}
if (common ==1)
{
comlist1[i][comlist1n[i]] = xnode;
comlist1n[i]++;
//printf("1 dependent to node %d is %s\n",
// i, t1.taxon[comlist1[i][comlist1n[i]-1]]);
}
active_n[xnode] = 0;
}
else
{
for (j = 0; j < t1.noat[xnode]; j++)
{
active_n[t1.down[xnode][j]] = 1;
}
active_n[xnode] = 0;
}
}
}
}
}
// make a full list of term taxa from each node:
// tree2:
for (i = 0; i < t2.nnodes; i++)
{
if (t2.depth[i] > t2md) t2md = t2.depth[i];
// need to clear the node names - they could cause confusion
// when bladjing, beacause the default names are the same for both
// trees
if (t2.noat[i] > 0) strcpy(t2.taxon[i], ".");
// these will get unmaned: see fy2new
}
active_n = ivector(0, t2.nnodes-1);
for (i = 0; i < t2.nnodes; i++)
{
active_n[i] = 1;
comlist2n[i] = 0;
for (depth = t2.depth[i]; depth <= t2md; depth++)
{
for (xnode = 0; xnode < t2.nnodes; xnode++)
{
if ( (t2.depth[xnode] == depth) && (active_n[xnode] == 1) )
{
// first we check to see if we have reached a tip
if (t2.noat[xnode] == 0)
{
// test to see that it is a common spp to tree 2
common = 0;
for (j = 0; j < t1.termtaxa; j++)
{
if (strcmp(t2.taxon[xnode], t1.taxalist[j]) == 0)\
common = 1;
}
if (common ==1)
{
comlist2[i][comlist2n[i]] = xnode;
comlist2n[i]++;
//printf("2 dependent to node %d is %s\n",
// i, t2.taxon[comlist2[i][comlist2n[i]-1]]);
}
active_n[xnode] = 0;
}
else
{
for (j = 0; j < t2.noat[xnode]; j++)
{
active_n[t2.down[xnode][j]] = 1;
}
active_n[xnode] = 0;
}
}
}
}
}
// Now, compare the nodes (once only for each pair)
for (i = 0; i < t1.nnodes; i++)
{
for (j = 0; j < t2.nnodes; j++)
{
// initialize:
for (p = 0; p < comlist1n[i]; p++) matched1[p] = 0;
for (q = 0; q < comlist2n[j]; q++) matched2[q] = 0;
// here's the crux - each one must have the same sublist to be valid
for (p = 0; p < comlist1n[i]; p++)
{
for(q= 0; q < comlist2n[j]; q++)
{
if (strcmp(t1.taxon[comlist1[i][p]],
t2.taxon[comlist2[j][q]] ) ==0 )
{
matched1[p] = 1;
matched2[q] = 1;
}
}
}
// check matches
matches1 = 0;
matches2 = 0;
for (p = 0; p < comlist1n[i]; p++)
{
if (matched1[p] == 1) matches1++;
}
for (q = 0; q < comlist2n[j]; q++)
{
if (matched2[q] == 1) matches2++;
}
if ( (matches1 == comlist1n[i]) && (matches2 == comlist2n[j]) && \
(matches1 > 1) && (matches2 > 1))
{
sprintf(tmp, "match%d", matchcode++);
//printf("tree1node%d matches with tree2node%d\n", i, j);
// more correct, but need to just use nodenames for r8s:
// strcat(t1.notes[i], tmp); strcat(t1.notes[i], " ");
// strcat(t2.notes[j], tmp); strcat(t2.notes[j], " ");
// for bladj (note the last one overrides the previous - this
// will general be correct
strcpy(t1.taxon[i], tmp);
strcpy(t2.taxon[j], tmp);
}
}
}
// Unname the "." node names (a hack)
for (i = 0; i < t1.nnodes; i++)
{
if (!strcmp(t1.taxon[i], ".")) strcpy(t1.taxon[i], "");
}
for (i = 0; i < t2.nnodes; i++)
{
if (!strcmp(t2.taxon[i], ".")) strcpy(t2.taxon[i], "");
}
printf("#NEXUS\n\nBEGIN TREES;\nTREE tree1 = ");
Fy2newRec(t1);
printf("TREE tree2 = ");
Fy2newRec(t2);
printf("END;\n");
Out[0] = t1;
//WriteNexus(Out, 1, InS, 0 , InC, 0 );
Out[0] = t2;
//WriteNexus(Out, 1, InS, 0 , InC, 0 );
}
void Bladj(phylo Intree)
{
int i, j, q, z, l = 0;
int *action;
int *AgeFixed;
char nameI[50];
float ageI;
int matched;
char line[201]; // array of characters from input line
int lineending;
// Dimension things:
action = ivector(0, Intree.nnodes -1);
AgeFixed = ivector(0, Intree.nnodes -1);
// Fix ages for nodes of terminal taxa in Phylogeny:
for (i = 0; i < Intree.nnodes; i++)
{
// terminal nodes
if (Intree.noat[i] == 0)
{
Intree.age[i] = 0.0;
AgeFixed[i] = 1;
}
else
{
Intree.age[i] = 99999.9;
AgeFixed[i] = 0;
}
}
// pre-read
lineending = whatnewline(INFILEA);
//Fix node ages for nodes found in ages file
Fa = fopen(INFILEA, "r");
while (myfgets(line, 200, Fa, lineending) != NULL)
{
sscanf(line, "%s %f", nameI, &ageI); // string
matched = 0;
for (z = 0; z < Intree.nnodes; z++)
{
if (strcmp(Intree.taxon[z], nameI) == 0)
{
Intree.age[z] = ageI;
AgeFixed[z] = 1;
matched = 1;
}
}
}
fclose(Fa);
//TODO will crash if no name/age for deepest node, need to add check for this
// The algorithm:
// 1. create network of fixed age nodes between the root and the other
// fixed age nodes, choosing the order of nodes to operate on first
// using age, then number of intervening nodes.
for (i = 0; i < Intree.nnodes; i++)
{
q = 0;
for (j = i+1; j < Intree.nnodes; j++)
{
// find all the line-of-site ages
action[q] = 0;
// correct for errors in ages
if ((LineOfSight(Intree, AgeFixed, i, j) == 1) && \
(Intree.age[j] >= Intree.age[i])) AgeFixed[j] = 0;
if ((AgeFixed[j] == 1) && (LineOfSight(Intree, AgeFixed, i, j) == 1))
{
// printf("%d+%d ",i, j);
action[q] = j;
q++;
}
}
// Now sort the action
SortAction(Intree, action, q, i);
// Adjust lengths
for (l = 0; l < q; l++)
{
Adjust(Intree, AgeFixed, i, action[l]);
//printf("i%d action%d\n",i, action[l]);
}
}
if (FYOUT) FyOut(Intree) ;
else Fy2newRec(Intree);
}
// -------------- WriteNexus ------------------
void WriteNexus(phylo P[], int ntree, sample S, int nsamp, traits T, int ntrf)
{
// Mesquite style!
time_t rawtime;
int i, j, q, k, x, pass, present;
int makedisc, makecont;
float abnd;
int nterm = 0;
phylo WN[ntree];
char tmp[MAXTAXONLENGTH+10];
for (i = 0; i < ntree; i++)
{
WN[i] = P[i]; // inefficient to make copy so much, but need to
// to create third dimension of taxon array
// reassign the pointer to a new space - free this!
WN[i].taxon = cmatrix(0, P[0].nnodes-1, 0, MAXTAXONLENGTH+10);
}
// determine number of terminal taxa - assume all trees contain same taxa
for (i = 0; i < P[0].nnodes; i++)
{
if (P[0].noat[i] == 0) nterm++;
}
time ( &rawtime );
strncpy(tmp , ctime(&rawtime), 24);
printf("#NEXUS\n[output from phylocom, written %s]\n\n", tmp );
printf("BEGIN TAXA;\n");
if (TreeView == 0) printf("TITLE Phylocom_Phylogeny_Taxa;\n"); // Needed for correct Mesquite grammar, but V1.1 busted! Will not read interior names correctly.
printf("\tDIMENSIONS NTAX=%d;\n\tTAXLABELS\n\t", nterm);
for (i = 0; i < P[0].nnodes; i++)
{
if (P[0].noat[i] == 0) printf(" %s", P[0].taxon[i]);
}
printf(";\nEND;\n\n");
if (nsamp > 0)
{
// Characters
printf("BEGIN CHARACTERS;\n\tTITLE Phylocom_Presence_in_Sample;\n\tDIMENSIONS NCHAR=%d;\n\tFORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = \" 0 1\";\n", S.nsamples);
printf("\tCHARSTATELABELS\n\t\t");
printf("%d %s", 1, S.pname[0]);
for (i = 1; i < S.nsamples; i++)
{
printf(", %d %s", i+1, S.pname[i]);
}
printf(";\n\tMATRIX\n");
for (i = 0; i < P[0].nnodes; i++)
{
if (P[0].noat[i] == 0)
{
printf("\t%s\t" , P[0].taxon[i]);
for (j = 0; j < S.nsamples; j++)
{
present = 0;
for (k = 0; k < S.srec[j]; k++)
{
if (strcmp(S.taxa[S.id[j][k]], P[0].taxon[i]) == 0) present = 1;
}
printf("%d", present);
}
printf("\n");
}
}
printf(";\nEND;\n\n");
// Abundances as continuous
printf("BEGIN CHARACTERS;\n\tTITLE Phylocom_Abundance_in_Sample;\n\tDIMENSIONS NCHAR=%d;\n\tFORMAT DATATYPE = CONTINUOUS GAP = - MISSING = ?;\n", S.nsamples);
printf("\tCHARSTATELABELS\n\t\t");
printf("%d %s", 1, S.pname[0]);
for (i = 1; i < S.nsamples; i++)
{
printf(", %d %s", i+1, S.pname[i]);
}
printf(";\n\tMATRIX\n");
for (i = 0; i < P[0].nnodes; i++)
{
if (P[0].noat[i] == 0)
{
printf("\t%s\t" , P[0].taxon[i]);
for (j = 0; j < S.nsamples; j++)
{
abnd = 0.0;
for (k = 0; k < S.srec[j]; k++)
{
if (strcmp(S.taxa[S.id[j][k]], P[0].taxon[i]) == 0) abnd = (float) S.abund[j][k];
}
printf(" %f", abnd);
}
printf("\n");
}
}
printf(";\nEND;\n\n");
}
if (ntrf > 0)
{
makedisc = 0;
makecont = 0;
pass = 0;
for (i = 0; i < T.ntraits; i++)
{
if ((T.type[i] == 0) || (T.type[i] == 1) || (T.type[i] == 2)) makedisc++;
if (T.type[i] == 3) makecont++;
}
if (makedisc > 0)
{
// Discrete Traits
printf("BEGIN CHARACTERS;\n\tTITLE Phylocom_Discrete_Traits;\n\tDIMENSIONS NCHAR=%d;\n\tFORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = \" 0 1 2 3 4 5 6 7 8 9\";\n", makedisc);
x = 1;
printf("\tCHARSTATELABELS\n\t\t");
// first one
for (i = 0; i < T.ntraits; i++)
{
if ((T.type[i] == 0) || (T.type[i] == 1) || (T.type[i] == 2))
{
printf("%d %s", x, T.trname[i]);
x++;
pass = i;
break;
}
}
for (i = pass+1; i < T.ntraits; i++)
{
if ((T.type[i] == 0) || (T.type[i] == 1) || (T.type[i] == 2))
{
printf(", %d %s", x, T.trname[i]);
x++;
}
}
printf(";\n\tMATRIX\n");
for (i = 0; i < T.ntaxa; i++)
{
printf("\t%s\t" , T.taxon[i]);
for (j = 0; j < T.ntraits; j++)
{
if ((T.type[j] == 0) || (T.type[j] == 1) || (T.type[j] == 2))
{
printf("%d", (int) T.tr[i][j]);
}
}
printf("\n");
}
printf(";\nEND;\n\n");
}
if (makecont > 0)
{
// Continous Traits
printf("BEGIN CHARACTERS;\n\tTITLE Phylocom_Continuous_Traits;\n\tDIMENSIONS NCHAR=%d;\n\tFORMAT DATATYPE = CONTINUOUS GAP = - MISSING = ?;\n", makecont);
x=1;
printf("\tCHARSTATELABELS\n\t\t");
// first one
for (i = 0; i < T.ntraits; i++)
{
if (T.type[i] == 3)
{
printf("%d %s", x, T.trname[i]);
x++;
pass = i;
break;
}
}
for (i = pass+1; i < T.ntraits; i++)
{
if (T.type[i] == 3)
{
printf(", %d %s", x, T.trname[i]);
x++;
}
}
printf(";\n\tMATRIX\n");
for (i = 0; i < T.ntaxa; i++)
{
printf("\t%s\t" , T.taxon[i]);
for (j = 0; j < T.ntraits; j++)
{
if (T.type[j] == 3)
{
printf(" %f", T.tr[i][j]);
}
}
printf("\n");
}
printf(";\nEND;\n\n");
}
}
printf("BEGIN TREES;\n");
if (TreeView == 0) printf("\tTITLE Phylocom_Phylogenies;\n\tLINK Taxa = Phylocom_Phylogeny_Taxa;\n"); // Ditto!
printf("\tTRANSLATE\n\t");
for (q = 0; q < ntree; q++)
{
j = 0;
for (i = 0; i < P[0].nnodes; i++)
{
if (P[0].noat[i] == 0)
{
j++;
if (q == 0)
{
if (i == P[0].nnodes-1) printf(" %d %s;\n", j, P[0].taxon[i]);
else printf(" %d %s,", j, P[0].taxon[i]);
}
sprintf(tmp, "%d", j);
strcpy(WN[q].taxon[i], tmp);
}
else if ((strcmp(P[q].taxon[i], "") != 0) && \
(strcmp(P[q].taxon[i], ".") != 0))
{
strcpy(WN[q].taxon[i], "'");
strcat(WN[q].taxon[i], P[q].taxon[i]);
strcat(WN[q].taxon[i], "'");
}
else strcpy(WN[q].taxon[i], "");
// test if (strcmp(WN[q].notes[i], "") != 0) printf("%s\n", WN[q].notes[i]);
}
}
for (q = 0; q < ntree; q++)
{
printf("\tTREE %s = ", WN[q].phyname);
Fy2newRec(WN[q]);
free_cmatrix(WN[q].taxon, 0, P[0].nnodes-1, 0, MAXTAXONLENGTH+10);
}
printf("END;\n");
printf("\nBEGIN PHYLOCOM;\n\tTITLE Phylocom_Main;\n\tDATA\n");
for (i = 0; i < S.nsamples; i++)
{
for (j = 0; j < S.srec[i]; j++)
{
printf("%s\t%d\t%s\n", S.pname[i], S.abund[i][j], S.taxa[S.id[i][j]]);
}
}
printf(";\nEND;\n");
//free_cmatrix(WN.taxon, 0, P.nnodes-1, 0, MAXTAXONLENGTH+10);
}
