- * Returns a boolean indicating whether the reference annotation is active.
- *
- * @return
- */
- public boolean referenceAnnotationIsActive()
- {
- String status;
- status = fileProperties.get(REFERENCE_ANNOTATION);
- if (status == null)
- {
- return false;
- }
- switch (status)
- {
- case YES:
- return true;
- case NO:
- return false;
- default:
- return false;
- }
-
- }
-
- /**
- * Returns a boolean indicating whether the mask value annotation is active.
- *
- * @return
- */
- public boolean maskValueIsActive()
- {
- String status;
- status = fileProperties.get(MASKED_VALUE);
- if (status == null)
- {
- return false;
- }
- switch (status)
- {
- case YES:
- return true;
- case NO:
- return false;
- default:
- return false;
- }
-
- }
-
- /**
- * Returns a boolean indicating whether the consensus residue annotation is
- * active.
- *
- * @return
- */
- public boolean consensusResidueIsActive()
- {
- String status;
- status = fileProperties.get(CONSENSUS_RESIDUE);
- if (status == null)
- {
- return false;
- }
- switch (status)
- {
- case YES:
- return true;
- case NO:
- return false;
- default:
- return false;
- }
-
- }
-
- /**
- * Returns a boolean indicating whether the consensus structure annotation is
- * active.
- *
- * @return
- */
- public boolean consensusStructureIsActive()
- {
- String status;
- status = fileProperties.get(CONSENSUS_STRUCTURE);
- if (status == null)
- {
- return false;
- }
- switch (status)
- {
- case YES:
- return true;
- case NO:
- return false;
- default:
- return false;
- }
-
- }
-
- /**
- * Returns a boolean indicating whether the MAP annotation is active.
- *
- * @return
- */
- public boolean mapIsActive()
- {
- String status;
- status = fileProperties.get(MAP);
- if (status == null)
- {
- return false;
- }
- switch (status)
- {
- case YES:
- return true;
- case NO:
- return false;
- default:
- return false;
- }
-
- }
-
- /**
- * Sets the alignment column of the specified node.
- *
- * @param nodeIndex
- *
- * @param column
- *
- */
- public void setAlignmentColumn(int nodeIndex, int column)
- {
- int currentCol = getNodeAlignmentColumn(nodeIndex);
- nodeLookup.remove(currentCol);
- nodes.get(nodeIndex).setAlignmentColumn(column);
- nodeLookup.put(column, nodeIndex);
- }
-
- /**
- * Clears all data in the node lookup map
- */
- public void emptyNodeLookup()
- {
- nodeLookup = new HashMap<>();
- }
-
-
- /**
- * 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);
- }
-
- /**