- * Sets the alignment column of the specified node
- *
- * @param nodeIndex
- *
- * @param column
- *
- */
- public void setAlignmentColumn(HMMNode node, int column)
- {
- node.setAlignmentColumn(column);
- nodeLookup.put(column, node);
- }
-
- public void updateMapping(char[] sequence)
- {
- int nodeNo = 1;
- int column = 0;
- synchronized (nodeLookup)
- {
- clearNodeLookup();
- for (char residue : sequence)
- {
- if (!Comparison.isGap(residue))
- {
- HMMNode node = nodes.get(nodeNo);
- if (node == null)
- {
- // error : too few nodes for sequence
- break;
- }
- setAlignmentColumn(node, column);
- nodeNo++;
- }
- column++;
- }
- }
- }
-
- /**
- * Clears all data in the node lookup map
- */
- public void clearNodeLookup()
- {
- nodeLookup.clear();
- }
-
- /**
- * Sets the reference annotation at a given node
- *
- * @param nodeIndex
- * @param value
- */
- public void setReferenceAnnotation(int nodeIndex, char value)
- {
- nodes.get(nodeIndex).setReferenceAnnotation(value);
- }
-
- /**
- * Sets the consensus residue at a given node
- *
- * @param nodeIndex
- * @param value
- */
- public void setConsensusResidue(int nodeIndex, char value)
- {
- nodes.get(nodeIndex).setConsensusResidue(value);
- }
-
- /**
- * Sets the consensus structure at a given node
- *
- * @param nodeIndex
- * @param value
- */
- public void setConsensusStructure(int nodeIndex, char value)
- {
- nodes.get(nodeIndex).setConsensusStructure(value);
- }
-
- /**
- * Sets the mask value at a given node
- *
- * @param nodeIndex
- * @param value
- */
- public void setMaskValue(int nodeIndex, char value)
- {
- nodes.get(nodeIndex).setMaskValue(value);
- }
-
- /**