package jalview.datamodel;
+import java.util.ArrayList;
import java.util.HashMap;
+import java.util.List;
import java.util.Map;
/**
- * Data structure to hold a HMM file
- */
-/**
+ * Data structure which stores a hidden Markov model. Currently contains file
+ * properties as well, not sure whether these should be transferred to the
+ * HMMFile class
+ *
* @author TZVanaalten
*
*/
public class HiddenMarkovModel
{
- // Stores file properties
- private Map<String, String> fileProperties = new HashMap<>();
+ // Stores file properties. Do not directly access this field as it contains
+ // only string value - use the getter methods. For example, to find the length
+ // of theHMM, use getModelLength()to return an int value
+ Map<String, String> fileProperties = new HashMap<>();
+
+ // contains all of the symbols used in this model. The index of each symbol
+ // represents its lookup value
+ List<Character> symbols = new ArrayList<>();
+
+ // contains information for each node in the model. The begin node is at index
+ // 0. Node 0 contains average emission probabilities for each symbol
+ List<HMMNode> nodes = new ArrayList<>();
+
+ // contains the HMM node for each alignment column, alignment columns start at
+ // index 0;
+ Map<Integer, Integer> nodeLookup = new HashMap<>();
+
+ // contains the symbol index for each symbol
+ Map<Character, Integer> symbolIndexLookup = new HashMap<>();
+
+ final static String YES = "yes";
+
+ final static String NO = "no";
+
+ // keys for file properties hashmap
+ private final String NAME = "NAME";
+
+ private final String ACCESSION_NUMBER = "ACC";
+
+ private final String DESCRIPTION = "DESC";
+
+ private final String LENGTH = "LENG";
+
+ private final String MAX_LENGTH = "MAXL";
+
+ private final String ALPHABET = "ALPH";
+
+ private final String DATE = "DATE";
+
+ private final String COMMAND_LOG = "COM";
+
+ private final String NUMBER_OF_SEQUENCES = "NSEQ";
+
+ private final String EFF_NUMBER_OF_SEQUENCES = "EFFN";
+
+ private final String CHECK_SUM = "CKSUM";
+
+ private final String GATHERING_THRESHOLDS = "GA";
+
+ private final String TRUSTED_CUTOFFS = "TC";
+
+ private final String NOISE_CUTOFFS = "NC";
+
+ private final String STATISTICS = "STATS";
+
+ private final String COMPO = "COMPO";
+
+ private final String GATHERING_THRESHOLD = "GA";
+
+ private final String TRUSTED_CUTOFF = "TC";
+
+ private final String NOISE_CUTOFF = "NC";
+
+ private final String VITERBI = "VITERBI";
+
+ private final String MSV = "MSV";
+
+ private final String FORWARD = "FORWARD";
+
+ private final String MAP = "MAP";
+
+ private final String REFERENCE_ANNOTATION = "RF";
+
+ private final String CONSENSUS_RESIDUE = "CONS";
+
+ private final String CONSENSUS_STRUCTURE = "CS";
+
+ private final String MASKED_VALUE = "MM";
+
+ public static final int MATCHTOMATCH = 0;
+
+ public static final int MATCHTOINSERT = 1;
+
+ public static final int MATCHTODELETE = 2;
+
+ public static final int INSERTTOMATCH = 3;
+
+ public static final int INSERTTOINSERT = 4;
+
+ public static final int DELETETOMATCH = 5;
+
+ public static final int DELETETODELETE = 6;
+
+ String fileHeader;
+
+ public HiddenMarkovModel()
+ {
+
+ }
+
+ public HiddenMarkovModel(HiddenMarkovModel hmm)
+ {
+ super();
+ this.fileProperties = new HashMap<>(hmm.fileProperties);
+ this.symbols = new ArrayList<>(hmm.symbols);
+ this.nodes = new ArrayList<>(hmm.nodes);
+ this.nodeLookup = new HashMap<>(hmm.nodeLookup);
+ this.symbolIndexLookup = new HashMap<>(
+ hmm.symbolIndexLookup);
+ this.fileHeader = new String(hmm.fileHeader);
+ }
+
+ /**
+ * Gets the file header of the .hmm file this model came from.
+ *
+ * @return
+ */
+ public String getFileHeader()
+ {
+ return fileHeader;
+ }
+
+ /**
+ * Sets the file header of this model.
+ *
+ * @param header
+ */
+ public void setFileHeader(String header)
+ {
+ fileHeader = header;
+ }
+
+ /**
+ * Returns the map containing the matches between nodes and alignment column
+ * indexes.
+ *
+ * @return
+ *
+ */
+ public Map<Integer, Integer> getNodeLookup()
+ {
+ return nodeLookup;
+ }
+
+ /**
+ * Returns the list of symbols used in this hidden Markov model.
+ *
+ * @return
+ */
+ public List<Character> getSymbols()
+ {
+ return symbols;
+ }
+
+ /**
+ * Returns the file properties.
+ *
+ * @return
+ */
+ public Map<String, String> getFileProperties()
+ {
+ return fileProperties;
+ }
+
+ /**
+ * Gets the node in the hidden Markov model at the specified position.
+ *
+ * @param nodeIndex
+ * The index of the node requested. Node 0 optionally contains the
+ * average match emission probabilities across the entire model, and
+ * always contains the insert emission probabilities and state
+ * transition probabilities for the begin node. Node 1 contains the
+ * first node in the HMM that can correspond to a column in the
+ * alignment.
+ * @return
+ */
+ public HMMNode getNode(int nodeIndex)
+ {
+ return getNodes().get(nodeIndex);
+ }
+
+ /**
+ * Sets the list of symbols used in the hidden Markov model to the list
+ * specified.
+ *
+ * @param symbolsL
+ * The list of symbols to which the current list is to be changed.
+ *
+ */
+ public void setSymbols(List<Character> symbolsL)
+ {
+ this.symbols = symbolsL;
+ }
+
+ /**
+ * Returns the name of the sequence alignment on which the HMM is based.
+ *
+ * @return
+ */
+ public String getName()
+ {
+ return fileProperties.get(NAME);
+ }
+
+ /**
+ * Returns the accession number.
+ * @return
+ */
public String getAccessionNumber()
{
- return fileProperties.get("ACC");
+ return fileProperties.get(ACCESSION_NUMBER);
}
+ /**
+ * Returns a description of the sequence alignment on which the hidden Markov
+ * model is based.
+ *
+ * @return
+ */
public String getDescription()
{
- return fileProperties.get("DESC");
+ return fileProperties.get(DESCRIPTION);
}
- public int getModelLength()
+ /**
+ * Returns the length of the hidden Markov model.
+ *
+ * @return
+ */
+ public Integer getLength()
{
- return Integer.parseInt(fileProperties.get("LENG"));
+ if (fileProperties.get(LENGTH) == null)
+ {
+ return null;
+ }
+ return Integer.parseInt(fileProperties.get(LENGTH));
}
- public int getMaxInstanceLength()
+ /**
+ * Returns the max instance length within the hidden Markov model.
+ *
+ * @return
+ */
+ public Integer getMaxInstanceLength()
{
- return Integer.parseInt(fileProperties.get("MAXL"));
+ if (fileProperties.get(MAX_LENGTH) == null)
+ {
+ return null;
+ }
+ return Integer.parseInt(fileProperties.get(MAX_LENGTH));
}
- // gets type of symbol alphabet - "amino", "DNA", "RNA"
+ /**
+ * Returns the type of symbol alphabet - "amino", "DNA", "RNA" are the
+ * options. Other alphabets may be added.
+ *
+ * @return
+ */
public String getAlphabetType()
{
- return fileProperties.get("ALPH");
+ return fileProperties.get(ALPHABET);
+ }
+
+ /**
+ * Returns the date as a String.
+ *
+ * @return
+ */
+ public String getDate()
+ {
+ return fileProperties.get(DATE);
+ }
+
+ /**
+ * Returns the command line log.
+ *
+ * @return
+ */
+ public String getCommandLineLog()
+ {
+ return fileProperties.get(COMMAND_LOG);
}
- // returns boolean indicating whether the reference annotation character field
- // for each match state is valid or ignored
- public boolean getReferenceAnnotationFlag()
+ /**
+ * Returns the number of sequences on which the HMM was trained.
+ *
+ * @return
+ */
+ public Integer getNumberOfSequences()
{
- if (fileProperties.get("RF") == "yes")
+ if (fileProperties.get(NUMBER_OF_SEQUENCES) == null)
{
+ return null;
+ }
+ return Integer.parseInt(fileProperties.get(NUMBER_OF_SEQUENCES));
+ }
+
+ /**
+ * Returns the effective number of sequences on which the HMM was based.
+ *
+ * @param value
+ */
+ public Double getEffectiveNumberOfSequences()
+ {
+ if (fileProperties.get(LENGTH) == null)
+ {
+ return null;
+ }
+ return Double.parseDouble(fileProperties.get(EFF_NUMBER_OF_SEQUENCES));
+ }
+
+ /**
+ * Returns the checksum.
+ *
+ * @return
+ */
+ public Long getCheckSum()
+ {
+ if (fileProperties.get(LENGTH) == null)
+ {
+ return null;
+ }
+ return Long.parseLong(fileProperties.get(CHECK_SUM));
+ }
+
+ /**
+ * Returns the list of nodes in this HMM.
+ *
+ * @return
+ */
+ public List<HMMNode> getNodes()
+ {
+ return nodes;
+ }
+
+ /**
+ * Sets the list of nodes in this HMM to the given list.
+ *
+ * @param nodes
+ * The list of nodes to which the current list of nodes is being
+ * changed.
+ */
+ public void setNodes(List<HMMNode> nodes)
+ {
+ this.nodes = nodes;
+ }
+
+ /**
+ * Gets the match emission probability for a given symbol at a column in the
+ * alignment.
+ *
+ * @param alignColumn
+ * The index of the alignment column, starting at index 0. Index 0
+ * usually corresponds to index 1 in the HMM.
+ * @param symbol
+ * The symbol for which the desired probability is being requested.
+ * @return
+ *
+ */
+ public Double getMatchEmissionProbability(int alignColumn, char symbol)
+ {
+ int symbolIndex;
+ int nodeIndex;
+ Double probability;
+ if (!symbolIndexLookup.containsKey(symbol))
+ {
+ return 0d;
+ }
+ symbolIndex = symbolIndexLookup.get(symbol);
+ if (nodeLookup.containsKey(alignColumn))
+ {
+ nodeIndex = nodeLookup.get(alignColumn);
+ probability = getNode(nodeIndex).getMatchEmissions().get(symbolIndex);
+ return probability;
+ }
+ else
+ {
+ return 0d;
+ }
+
+ }
+
+ /**
+ * Gets the insert emission probability for a given symbol at a column in the
+ * alignment.
+ *
+ * @param alignColumn
+ * The index of the alignment column, starting at index 0. Index 0
+ * usually corresponds to index 1 in the HMM.
+ * @param symbol
+ * The symbol for which the desired probability is being requested.
+ * @return
+ *
+ */
+ public Double getInsertEmissionProbability(int alignColumn, char symbol)
+ {
+ int symbolIndex;
+ int nodeIndex;
+ Double probability;
+ if (!symbolIndexLookup.containsKey(symbol))
+ {
+ return 0d;
+ }
+ symbolIndex = symbolIndexLookup.get(symbol);
+ if (nodeLookup.containsKey(alignColumn))
+ {
+ nodeIndex = nodeLookup.get(alignColumn);
+ probability = getNode(nodeIndex).getInsertEmissions()
+ .get(symbolIndex);
+ return probability;
+ }
+ else
+ {
+ return 0d;
+ }
+
+ }
+
+ /**
+ * Gets the state transition probability for a given symbol at a column in the
+ * alignment.
+ *
+ * @param alignColumn
+ * The index of the alignment column, starting at index 0. Index 0
+ * usually corresponds to index 1 in the HMM.
+ * @param symbol
+ * The symbol for which the desired probability is being requested.
+ * @return
+ *
+ */
+ public Double getStateTransitionProbability(int alignColumn,
+ int transition)
+ {
+ int nodeIndex;
+ Double probability;
+ if (nodeLookup.containsKey(alignColumn))
+ {
+ nodeIndex = nodeLookup.get(alignColumn);
+ probability = getNode(nodeIndex).getStateTransitions()
+ .get(transition);
+ return probability;
+ }
+ else
+ {
+ return 0d;
+ }
+
+ }
+
+ /**
+ * Returns the alignment column linked to the node at the given index.
+ *
+ * @param nodeIndex
+ * The index of the node, starting from index 1. Index 0 is the begin
+ * node, which does not correspond to a column in the alignment.
+ * @return
+ */
+ public Integer getNodeAlignmentColumn(int nodeIndex)
+ {
+ Integer value = nodes.get(nodeIndex).getAlignmentColumn();
+ return value;
+ }
+
+ /**
+ * Returns the consensus residue at the specified node.
+ *
+ * @param nodeIndex
+ * The index of the specified node.
+ * @return
+ */
+ public char getConsensusResidue(int nodeIndex)
+ {
+ char value = nodes.get(nodeIndex).getConsensusResidue();
+ return value;
+ }
+
+ /**
+ * Returns the consensus at a given alignment column. If the character is
+ * lower case, its emission probability is less than 0.5.
+ *
+ * @param columnIndex
+ * The index of the column in the alignment for which the consensus
+ * is desired. The list of columns starts at index 0.
+ * @return
+ */
+ public char getConsensusAtAlignColumn(int columnIndex)
+ {
+ char mostLikely = '-';
+ if (consensusResidueIsActive())
+ {
+
+ Integer index = findNodeIndex(columnIndex);
+ if (index == null)
+ {
+ return '-';
+ }
+ mostLikely = getNodes().get(index).getConsensusResidue();
+ return mostLikely;
+ }
+ else
+ {
+ double highestProb = 0;
+ for (char character : symbols)
+ {
+ Double prob = getMatchEmissionProbability(columnIndex, character);
+ if (prob > highestProb)
+ {
+ highestProb = prob;
+ mostLikely = character;
+ }
+ }
+ if (highestProb < 0.5)
+ {
+ mostLikely = Character.toLowerCase(mostLikely);
+ }
+ return mostLikely;
+ }
+
+ }
+
+ /**
+ * Returns the reference annotation at the specified node.
+ *
+ * @param nodeIndex
+ * The index of the specified node.
+ * @return
+ */
+ public char getReferenceAnnotation(int nodeIndex)
+ {
+ char value = nodes.get(nodeIndex).getReferenceAnnotation();
+ return value;
+ }
+
+ /**
+ * Returns the mask value at the specified node.
+ *
+ * @param nodeIndex
+ * The index of the specified node.
+ * @return
+ */
+ public char getMaskedValue(int nodeIndex)
+ {
+ char value = nodes.get(nodeIndex).getMaskValue();
+ return value;
+ }
+
+ /**
+ * Returns the consensus structure at the specified node.
+ *
+ * @param nodeIndex
+ * The index of the specified node.
+ * @return
+ */
+ public char getConsensusStructure(int nodeIndex)
+ {
+ char value = nodes.get(nodeIndex).getConsensusStructure();
+ return value;
+ }
+
+ /**
+ * Returns the average match emission probability for a given symbol
+ *
+ * @param symbolIndex
+ * The index of the symbol.
+ * @return
+ *
+ */
+ public double getAverageMatchEmission(int symbolIndex)
+ {
+ double value = nodes.get(0).getMatchEmissions().get(symbolIndex);
+ return value;
+ }
+
+ /**
+ * Returns the number of symbols in the alphabet used in this HMM.
+ *
+ * @return
+ */
+ public int getNumberOfSymbols()
+ {
+ return symbols.size();
+ }
+
+ /**
+ * Adds a file property.
+ *
+ * @param key
+ * @param value
+ */
+ public void addFileProperty(String key, String value)
+ {
+ fileProperties.put(key, value);
+ }
+
+ /**
+ * 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;
}
- return false;
+
}
- // returns boolean indicating whether the model mask annotation character
- // field
- // for each match state is valid or ignored
- public boolean getModelMaskedFlag()
+ /**
+ * Returns a boolean indicating whether the mask value annotation is active.
+ *
+ * @return
+ */
+ public boolean maskValueIsActive()
{
- if (fileProperties.get("MM") == "yes")
+ 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;
}
- return false;
+
}
- // returns boolean indicating whether the consensus residue field
- // for each match state is valid or ignored
- public boolean getConsensusResidueAnnotationFlag()
+ /**
+ * Returns a boolean indicating whether the consensus residue annotation is
+ * active.
+ *
+ * @return
+ */
+ public boolean consensusResidueIsActive()
{
- if (fileProperties.get("CONS") == "yes")
+ 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;
}
- return false;
+
}
- // returns boolean indicating whether the consensus structure character field
- // for each match state is valid or ignored
- public boolean getConsensusStructureAnnotationFlag()
+ /**
+ * Returns a boolean indicating whether the consensus structure annotation is
+ * active.
+ *
+ * @return
+ */
+ public boolean consensusStructureIsActive()
{
- if (fileProperties.get("CS") == "yes")
+ 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;
}
- return false;
+
}
- // returns boolean indicating whether the model mask annotation character
- // field
- // for each match state is valid or ignored
- public boolean getMapAnnotationFlag()
+ /**
+ * Returns a boolean indicating whether the MAP annotation is active.
+ *
+ * @return
+ */
+ public boolean mapIsActive()
{
- if (fileProperties.get("MAP") == "yes")
+ String status;
+ status = fileProperties.get(MAP);
+ if (status == null)
{
+ return false;
+ }
+ switch (status)
+ {
+ case YES:
return true;
+ case NO:
+ return false;
+ default:
+ return false;
}
- return false;
+
}
- // not sure whether to implement this
- // public Date getDate()
- // {
+ /**
+ * 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<>();
+ }
- // not sure whether to implement this
- // public String getCommandLineLog()
- // {
- // }
+ /**
+ * Sets the reference annotation at a given node.
+ *
+ * @param nodeIndex
+ * @param value
+ */
+ public void setReferenceAnnotation(int nodeIndex, char value)
+ {
+ nodes.get(nodeIndex).setReferenceAnnotation(value);
+ }
- // gets the number of sequences that the HMM was trained on
- public int getSequenceNumber()
+ /**
+ * Sets the consensus residue at a given node.
+ *
+ * @param nodeIndex
+ * @param value
+ */
+ public void setConsensusResidue(int nodeIndex, char value)
{
- return Integer.parseInt(fileProperties.get("NSEQ"));
+ nodes.get(nodeIndex).setConsensusResidue(value);
}
- // gets the effective number determined during sequence weighting
- public int getEffectiveSequenceNumber()
+ /**
+ * Sets the consensus structure at a given node.
+ *
+ * @param nodeIndex
+ * @param value
+ */
+ public void setConsensusStructure(int nodeIndex, char value)
{
- return Integer.parseInt(fileProperties.get("EFFN"));
+ nodes.get(nodeIndex).setConsensusStructure(value);
}
- public int getCheckSum()
+ /**
+ * Sets the mask value at a given node.
+ *
+ * @param nodeIndex
+ * @param value
+ */
+ public void setMaskValue(int nodeIndex, char value)
{
- return Integer.parseInt(fileProperties.get("CKSUM"));
+ nodes.get(nodeIndex).setMaskValue(value);
}
- // need to ask if BigDecimal is best decimal type for this purpose
- // and how to limit number of decimals
- public double getGatheringThresholdGA1()
+ /**
+ * Temporary implementation, should not be used.
+ *
+ * @return
+ */
+ public String getGatheringThreshold()
{
- return Double.parseDouble((fileProperties.get("GA1")));
+ String value;
+ value = fileProperties.get("GA");
+ return value;
}
- public void put(String key, String value)
+ /**
+ * Temporary implementation, should not be used.
+ *
+ * @return
+ */
+ public String getNoiseCutoff()
{
- fileProperties.put(key, value);
+ String value;
+ value = fileProperties.get("NC");
+ return value;
+ }
+
+ /**
+ * Temporary implementation, should not be used.
+ *
+ * @return
+ */
+ public String getTrustedCutoff()
+ {
+ String value;
+ value = fileProperties.get("TC");
+ return value;
+ }
+
+ /**
+ * Temporary implementation, should not be used.
+ *
+ * @return
+ */
+ public String getViterbi()
+ {
+ String value;
+ value = fileProperties.get(VITERBI);
+ return value;
+ }
+
+ /**
+ * Temporary implementation, should not be used.
+ *
+ * @return
+ */
+ public String getMSV()
+ {
+ String value;
+ value = fileProperties.get(MSV);
+ return value;
+ }
+
+ /**
+ * Temporary implementation, should not be used.
+ *
+ * @return
+ */
+ public String getForward()
+ {
+ String value;
+ value = fileProperties.get(FORWARD);
+ return value;
+ }
+
+ /**
+ * Sets the activation status of the MAP annotation.
+ *
+ * @param status
+ */
+ public void setMAPStatus(boolean status)
+ {
+ fileProperties.put(MAP, status ? YES : NO);
+ }
+
+ /**
+ * Sets the activation status of the reference annotation.
+ *
+ * @param status
+ */
+ public void setReferenceAnnotationStatus(boolean status)
+ {
+ fileProperties.put(REFERENCE_ANNOTATION, status ? YES : NO);
+ }
+
+ /**
+ * Sets the activation status of the mask value annotation.
+ *
+ * @param status
+ */
+ public void setMaskedValueStatus(boolean status)
+ {
+ fileProperties.put(MASKED_VALUE, status ? YES : NO);
+ }
+
+ /**
+ * Sets the activation status of the consensus residue annotation.
+ *
+ * @param status
+ */
+ public void setConsensusResidueStatus(boolean status)
+ {
+ fileProperties.put(CONSENSUS_RESIDUE, status ? YES : NO);
+ }
+
+ /**
+ * Sets the activation status of the consensus structure annotation.
+ *
+ * @param status
+ */
+ public void setConsensusStructureStatus(boolean status)
+ {
+ fileProperties.put(CONSENSUS_STRUCTURE, status ? YES : NO);
+ }
+
+ /**
+ * Finds the index of the node in a hidden Markov model based on the column in
+ * the alignment
+ *
+ * @param alignmentColumn
+ * The index of the column in the alignment, with the indexes
+ * starting from 0.
+ */
+
+ public Integer findNodeIndex(int alignmentColumn)
+ {
+ Integer index;
+ index = nodeLookup.get(alignmentColumn);
+ return index;
+ }
+
+ /**
+ * Finds the String values of a boolean. "yes" for true and "no" for false.
+ *
+ * @param value
+ * @return
+ */
+ public static String findStringFromBoolean(boolean value)
+ {
+ if (value)
+ {
+ return YES;
+ }
+ else
+ {
+ return NO;
+ }
+ }
+
+
+
+ /**
+ * Returns the consensus sequence based on the most probable symbol at each
+ * position. The sequence is adjusted to match the length of the existing
+ * sequence alignment. Gap characters are used as padding.
+ *
+ * @param length
+ * The length of the longest sequence in the existing alignment.
+ * @return
+ */
+ public Sequence getConsensusSequence()
+ {
+ int start;
+ int end;
+ int modelLength;
+ start = getNodeAlignmentColumn(1);
+ modelLength = getLength();
+ end = getNodeAlignmentColumn(modelLength);
+ char[] sequence = new char[end + 1];
+ for (int index = 0; index < end + 1; index++)
+ {
+ Character character;
+
+ character = getConsensusAtAlignColumn(index);
+
+ if (character == null || character == '-')
+ {
+ sequence[index] = '-';
+ }
+ else
+ {
+ sequence[index] = Character.toUpperCase(character);
+ }
+ }
+
+
+ Sequence seq = new Sequence(getName(), sequence, start,
+ end);
+ return seq;
+ }
+
+
+ /**
+ * Initiates a HMM consensus sequence
+ *
+ * @return A new HMM consensus sequence
+ */
+ public SequenceI initHMMSequence()
+ {
+ Sequence consensus = getConsensusSequence();
+ consensus.setIsHMMConsensusSequence(true);
+ consensus.setHMM(this);
+ return consensus;
+ }
+
+ public int getSymbolIndex(char c)
+ {
+ return symbolIndexLookup.get(c);
+ }
+
+ public void setSymbolIndex(Character c, Integer i)
+ {
+ symbolIndexLookup.put(c, i);
}
}
+
git://source.jalview.org / jalview.git / blobdiff