- public void addFileProperty(String key, String value)
- {
- fileProperties.put(key, value);
- }
-
- 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;
- }
-
- }
-
- 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;
- }
-
- }
-
- 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;
- }
-
- }
-
- 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;
- }
-
- }
-
- 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;
- }
-
- }
-
- public void setAlignmentColumn(int nodeIndex, int column)
- {
- nodes.get(nodeIndex).setAlignmentColumn(column);
- }
-
- public void setReferenceAnnotation(int nodeIndex, char value)
- {
- nodes.get(nodeIndex).setReferenceAnnotation(value);
- }
-
- public void setConsensusResidue(int nodeIndex, char value)
- {
- nodes.get(nodeIndex).setConsensusResidue(value);
- }
-
- public void setConsensusStructure(int nodeIndex, char value)
- {
- nodes.get(nodeIndex).setConsensusStructure(value);
- }
-
- public void setMaskValue(int nodeIndex, char value)
- {
- nodes.get(nodeIndex).setMaskValue(value);
- }
-
- public String getGatheringThreshold()