+++ /dev/null
-/**
- * Author: Mark Larkin
- *
- * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
- */
-#ifdef HAVE_CONFIG_H
- #include "config.h"
-#endif
-#include "ClusterTreeOutput.h"
-
-namespace clustalw
-{
-
-ClusterTreeOutput::ClusterTreeOutput(SeqInfo* seqInfo, int boot)
-: bootstrap(boot)
-{
- firstSeq = seqInfo->firstSeq;
- lastSeq = seqInfo->lastSeq;
- numSeqs = seqInfo->numSeqs;
-}
-
-void ClusterTreeOutput::printTreeDesc(PhyloTree* phyloTree)
-{
- for(int i = 1; i <= numSeqs; i++)
- {
- for(int j = 1; j <= numSeqs; j++)
- {
- cout << " " << phyloTree->treeDesc[i][j];
- }
- cout << "\n";
- }
-}
-
-
-/**
- * The function printPhylipTree is used to print out the unrooted clustered tree in
- * phylip format.
- * @param phyloTree A pointer to the PhyloTree struct that contains the description of the
- * tree.
- * @param tree The file to print the phylip tree to. Must be open!
- * @param alignPtr The alignment object. Needed for the names.
- * @param distMat The distance matrix that was used for the generation of the cluster.
- * @param bootTotals Holds the bootstrap values. Only used if the tree has been bootstrapped
- */
-void ClusterTreeOutput::printPhylipTree(PhyloTree* phyloTree, ofstream* tree,
- Alignment *alignPtr, DistMatrix* distMat, vector<int>* bootTotals)
-{
- int oldRow;
- if (lastSeq - firstSeq + 1 == 2)
- {
- (*tree) << "(" << alignPtr->getName(firstSeq) << ":" << fixed <<setprecision(5)
- << (*distMat)(firstSeq, firstSeq + 1) << "," << alignPtr->getName(firstSeq + 1)
- << ":" << fixed << setprecision(5) << (*distMat)(firstSeq, firstSeq + 1)
- << ");";
- return ;
- }
-
- (*tree) << "(\n";
-
- oldRow = twoWaySplit(phyloTree, tree, lastSeq - firstSeq + 1 - 2,
- 1, alignPtr, bootTotals);
-
- (*tree) << ":" << fixed << setprecision(5)
- << phyloTree->leftBranch[lastSeq - firstSeq + 1 - 2];
-
- if ((bootstrap == BS_BRANCH_LABELS) && (oldRow > 0) &&
- ((*bootTotals)[oldRow] > 0))
- {
- (*tree) << "[" << (*bootTotals)[oldRow] << "]";
- }
- (*tree) << ",\n";
-
- oldRow = twoWaySplit(phyloTree, tree, lastSeq - firstSeq + 1 - 2,
- 2, alignPtr, bootTotals);
-
- (*tree) << ":" << fixed << setprecision(5)
- << phyloTree->leftBranch[lastSeq - firstSeq + 1 - 1];
-
- if ((bootstrap == BS_BRANCH_LABELS) && (oldRow > 0) &&
- ((*bootTotals)[oldRow] > 0))
- {
- (*tree) << "[" << (*bootTotals)[oldRow] << "]";
- }
- (*tree) << ",\n";
-
- oldRow = twoWaySplit(phyloTree, tree, lastSeq - firstSeq + 1 - 2,
- 3, alignPtr, bootTotals);
-
- (*tree) << ":" << fixed << setprecision(5)
- << phyloTree->leftBranch[lastSeq - firstSeq + 1];
-
- if ((bootstrap == BS_BRANCH_LABELS) && (oldRow > 0) &&
- ((*bootTotals)[oldRow] > 0))
- {
- (*tree) << "[" << (*bootTotals)[oldRow] << "]";
- }
- (*tree) << ")";
-
- if (bootstrap == BS_NODE_LABELS)
- {
- (*tree) << "TRICHOTOMY";
- }
- (*tree) << ";\n";
-}
-
-int ClusterTreeOutput::twoWaySplit(PhyloTree* phyloTree, ofstream* tree,
- int startRow, int flag, Alignment *alignPtr, vector<int>* bootTotals)
-{
- int row, newRow = 0, oldRow, col, testCol = 0;
- bool singleSeq;
-
- if (startRow != lastSeq - firstSeq + 1-2)
- {
- (*tree) << "(\n";
- }
-
- for (col = 1; col <= lastSeq - firstSeq + 1; col++)
- {
- if (phyloTree->treeDesc[startRow][col] == flag)
- {
- testCol = col;
- break;
- }
- }
-
- singleSeq = true;
- for (row = startRow - 1; row >= 1; row--)
- if (phyloTree->treeDesc[row][testCol] == 1)
- {
- singleSeq = false;
- newRow = row;
- break;
- }
-
- if (singleSeq)
- {
- phyloTree->treeDesc[startRow][testCol] = 0;
- (*tree) << alignPtr->getName(testCol + firstSeq - 1);
- if (startRow == lastSeq - firstSeq + 1 - 2)
- {
- return (0);
- }
-
- (*tree) << ":" << fixed << setprecision(5) << phyloTree->leftBranch[startRow]
- << ",\n";
- }
- else
- {
- for (col = 1; col <= lastSeq - firstSeq + 1; col++)
- {
- if ((phyloTree->treeDesc[startRow][col] == 1) &&
- (phyloTree->treeDesc[newRow][col] == 1))
- {
- phyloTree->treeDesc[startRow][col] = 0;
- }
- }
- oldRow = twoWaySplit(phyloTree, tree, newRow, 1, alignPtr, bootTotals);
-
- if (startRow == lastSeq - firstSeq + 1-2)
- {
- return (newRow);
- }
-
- (*tree) << ":" << fixed << setprecision(5) << phyloTree->leftBranch[startRow];
-
- if ((bootstrap == BS_BRANCH_LABELS) && ((*bootTotals)[oldRow] > 0))
- {
- (*tree) << "[" << (*bootTotals)[oldRow] << "]";
- }
-
- (*tree) << ",\n";
- }
-
-
- for (col = 1; col <= lastSeq - firstSeq + 1; col++)
- if (phyloTree->treeDesc[startRow][col] == flag)
- {
- testCol = col;
- break;
- }
-
- singleSeq = true;
- newRow = 0;
- for (row = startRow - 1; row >= 1; row--)
- if (phyloTree->treeDesc[row][testCol] == 1)
- {
- singleSeq = false;
- newRow = row;
- break;
- }
-
- if (singleSeq)
- {
- phyloTree->treeDesc[startRow][testCol] = 0;
- (*tree) << alignPtr->getName(testCol + firstSeq - 1);
- (*tree) << ":" << fixed << setprecision(5) << phyloTree->rightBranch[startRow]
- <<")\n";
- }
- else
- {
- for (col = 1; col <= lastSeq - firstSeq + 1; col++)
- {
- if ((phyloTree->treeDesc[startRow][col] == 1) &&
- (phyloTree->treeDesc[newRow][col] == 1))
- {
- phyloTree->treeDesc[startRow][col] = 0;
- }
- }
- oldRow = twoWaySplit(phyloTree, tree, newRow, 1, alignPtr, bootTotals);
- (*tree) << ":" << fixed << setprecision(5) << phyloTree->rightBranch[startRow];
-
- if ((bootstrap == BS_BRANCH_LABELS) && ((*bootTotals)[oldRow] > 0))
- {
- (*tree) << "[" << (*bootTotals)[oldRow] << "]";
- }
-
- (*tree) << ")\n";
- }
- if ((bootstrap == BS_NODE_LABELS) && ((*bootTotals)[startRow] > 0))
- {
- (*tree) << (*bootTotals)[startRow];
- }
-
- return (startRow);
-}
-
-void ClusterTreeOutput::printNexusTree(PhyloTree* phyloTree, ofstream* tree,
- Alignment *alignPtr, DistMatrix* distMat, vector<int>* bootTotals)
-{
- int i;
- int oldRow;
-
- (*tree) << "#NEXUS\n\n";
-
- (*tree) << "BEGIN TREES;\n\n";
- (*tree) << "\tTRANSLATE\n";
-
- for(i = 1; i < numSeqs; i++)
- {
- (*tree) << "\t\t" << i << "\t" << alignPtr->getName(i) <<",\n";
- }
- (*tree) << "\t\t" << numSeqs << "\t" << alignPtr->getName(numSeqs) <<"\n";
- (*tree) << "\t\t;\n";
-
- (*tree) << "\tUTREE PAUP_1= ";
-
- if(lastSeq - firstSeq + 1 == 2)
- {
- (*tree) << "(" << firstSeq << ":" << fixed << setprecision(5)
- << (*distMat)(firstSeq, firstSeq + 1) << "," << firstSeq + 1 << ":"
- << fixed << setprecision(5) << (*distMat)(firstSeq, firstSeq + 1) << ")";
- }
- else
- {
-
- (*tree) << "(";
-
- oldRow = twoWaySplitNexus(phyloTree, tree,
- lastSeq - firstSeq + 1 - 2, 1, alignPtr, bootTotals);
-
- (*tree) << ":" << fixed << setprecision(5)
- << phyloTree->leftBranch[lastSeq-firstSeq+1-2];
-
- if ((bootstrap == BS_BRANCH_LABELS) && (oldRow > 0) && ((*bootTotals)[oldRow]>0))
- {
- (*tree) << "[" << (*bootTotals)[oldRow] << "]";
- }
-
- (*tree) << ",";
-
- oldRow = twoWaySplitNexus(phyloTree, tree, lastSeq - firstSeq + 1 - 2, 2,
- alignPtr, bootTotals);
- (*tree) << ":" << fixed << setprecision(5)
- << phyloTree->leftBranch[lastSeq-firstSeq+1-1];
-
- if ((bootstrap==BS_BRANCH_LABELS) && (oldRow>0) && ((*bootTotals)[oldRow]>0))
- {
- (*tree) << "[" << (*bootTotals)[oldRow] << "]";
- }
-
- (*tree) << ",";
-
- oldRow = twoWaySplitNexus(phyloTree, tree,
- lastSeq-firstSeq+1-2, 3, alignPtr, bootTotals);
-
- (*tree) << ":" << fixed << setprecision(5)
- << phyloTree->leftBranch[lastSeq-firstSeq+1];
-
- if ((bootstrap==BS_BRANCH_LABELS) && (oldRow>0) && ((*bootTotals)[oldRow]>0))
- {
- (*tree) << "[" << (*bootTotals)[oldRow] << "]";
- }
-
- (*tree) << ")";
-
- if (bootstrap == BS_NODE_LABELS)
- {
- (*tree) << "TRICHOTOMY";
- }
- (*tree) << ";";
- }
- (*tree) << "\nENDBLOCK;\n";
-}
-
-int ClusterTreeOutput::twoWaySplitNexus(PhyloTree* phyloTree, ofstream* tree,
- int startRow, int flag, Alignment *alignPtr, vector<int>* bootTotals)
-{
- int row, newRow = 0, oldRow, col, testCol = 0;
- bool singleSeq;
-
- if (startRow != lastSeq - firstSeq + 1 - 2)
- {
- (*tree) << "(";
- }
-
- for (col = 1; col <= lastSeq - firstSeq + 1; col++)
- {
- if (phyloTree->treeDesc[startRow][col] == flag)
- {
- testCol = col;
- break;
- }
- }
-
- singleSeq = true;
- for (row = startRow - 1; row >= 1; row--)
- if (phyloTree->treeDesc[row][testCol] == 1)
- {
- singleSeq = false;
- newRow = row;
- break;
- }
-
- if (singleSeq)
- {
- phyloTree->treeDesc[startRow][testCol] = 0;
- (*tree) << testCol + firstSeq - 1;;
- if (startRow == lastSeq - firstSeq + 1-2)
- {
- return (0);
- }
-
- (*tree) << ":" << fixed << setprecision(5) << phyloTree->leftBranch[startRow] << ",";
- }
- else
- {
- for (col = 1; col <= lastSeq - firstSeq + 1; col++)
- {
- if ((phyloTree->treeDesc[startRow][col] == 1) &&
- (phyloTree->treeDesc[newRow][col] == 1))
- {
- phyloTree->treeDesc[startRow][col] = 0;
- }
- }
- oldRow = twoWaySplitNexus(phyloTree, tree, newRow, 1, alignPtr, bootTotals);
-
- if (startRow == lastSeq - firstSeq + 1-2)
- {
- return (newRow);
- }
-
- (*tree) << ":" << fixed << setprecision(5) << phyloTree->leftBranch[startRow];
- if ((bootstrap == BS_BRANCH_LABELS) && ((*bootTotals)[oldRow] > 0))
- {
- (*tree) << "[" << (*bootTotals)[oldRow] << "]";
- }
-
- (*tree) << ",";
- }
-
-
- for (col = 1; col <= lastSeq - firstSeq + 1; col++)
- if (phyloTree->treeDesc[startRow][col] == flag)
- {
- testCol = col;
- break;
- }
-
- singleSeq = true;
- newRow = 0;
- for (row = startRow - 1; row >= 1; row--)
- if (phyloTree->treeDesc[row][testCol] == 1)
- {
- singleSeq = false;
- newRow = row;
- break;
- }
-
- if (singleSeq)
- {
- phyloTree->treeDesc[startRow][testCol] = 0;
- (*tree) << testCol + firstSeq - 1;
- (*tree) << ":" << fixed << setprecision(5) << phyloTree->rightBranch[startRow] << ")";
- }
- else
- {
- for (col = 1; col <= lastSeq - firstSeq + 1; col++)
- {
- if ((phyloTree->treeDesc[startRow][col] == 1) &&
- (phyloTree->treeDesc[newRow][col] == 1))
- {
- phyloTree->treeDesc[startRow][col] = 0;
- }
- }
- oldRow = twoWaySplitNexus(phyloTree, tree, newRow, 1, alignPtr, bootTotals);
-
- (*tree) << ":" << fixed << setprecision(5) << phyloTree->rightBranch[startRow];
- if ((bootstrap == BS_BRANCH_LABELS) && ((*bootTotals)[oldRow] > 0))
- {
- (*tree) << "[" << (*bootTotals)[oldRow] << "]";
- }
-
- (*tree) << ")";
- }
- if ((bootstrap == BS_NODE_LABELS) && ((*bootTotals)[startRow] > 0))
- {
- (*tree) << (*bootTotals)[startRow];
- }
-
- return (startRow);
-}
-
-void ClusterTreeOutput::printTree(PhyloTree* phyloTree, ofstream* tree,
- vector<int>* totals)
-{
- int row, col;
-
- (*tree) << "\n";
-
- for (row = 1; row <= lastSeq - firstSeq + 1 - 3; row++)
- {
- (*tree) << " \n";
- for (col = 1; col <= lastSeq - firstSeq + 1; col++)
- {
- if (phyloTree->treeDesc[row][col] == 0)
- {
- (*tree) << "*";
- }
- else
- {
- (*tree) << ".";
- }
- }
- if ((*totals)[row] > 0)
- {
- (*tree) << setw(7) << (*totals)[row];
- }
- }
- (*tree) << " \n";
- for (col = 1; col <= lastSeq - firstSeq + 1; col++)
- {
- (*tree) << setw(1) << phyloTree->treeDesc[lastSeq - firstSeq + 1 -2][col];
- }
- (*tree) << "\n";
-}
-
-}
git://source.jalview.org / jabaws.git / blobdiff