package jalview.datamodel;
import jalview.gui.AlignFrame;
-import jalview.schemes.ResidueProperties;
import java.util.ArrayList;
import java.util.HashMap;
// 0. Node 0 contains average emission probabilities for each symbol
List<HMMNode> nodes = new ArrayList<>();
- // contains the HMM node for each alignment column
+ // 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
public HiddenMarkovModel(HiddenMarkovModel hmm)
{
super();
- this.fileProperties = hmm.fileProperties;
- this.symbols = hmm.symbols;
- this.nodes = hmm.nodes;
- this.nodeLookup = hmm.nodeLookup;
- this.symbolIndexLookup = hmm.symbolIndexLookup;
+ 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.numberOfSymbols = hmm.numberOfSymbols;
- this.fileHeader = hmm.fileHeader;
+ this.fileHeader = new String(hmm.fileHeader);
}
/**
return 0d;
}
symbolIndex = symbolIndexLookup.get(symbol);
- if (nodeLookup.containsKey(alignColumn + 1))
+ if (nodeLookup.containsKey(alignColumn))
{
- nodeIndex = nodeLookup.get(alignColumn + 1);
+ nodeIndex = nodeLookup.get(alignColumn);
probability = getNode(nodeIndex).getMatchEmissions().get(symbolIndex);
return probability;
}
return 0d;
}
symbolIndex = symbolIndexLookup.get(symbol);
- if (nodeLookup.containsKey(alignColumn + 1))
+ if (nodeLookup.containsKey(alignColumn))
{
- nodeIndex = nodeLookup.get(alignColumn + 1);
+ nodeIndex = nodeLookup.get(alignColumn);
probability = getNode(nodeIndex).getInsertEmissions()
.get(symbolIndex);
return probability;
int transitionIndex;
int nodeIndex;
Double probability;
- if (nodeLookup.containsKey(alignColumn + 1))
+ if (nodeLookup.containsKey(alignColumn))
{
- nodeIndex = nodeLookup.get(alignColumn + 1);
+ nodeIndex = nodeLookup.get(alignColumn);
probability = getNode(nodeIndex).getStateTransitions()
.get(transition);
return probability;
public Integer getNodeAlignmentColumn(int nodeIndex)
{
Integer value = nodes.get(nodeIndex).getAlignmentColumn();
- return value - 1;
+ return value;
}
/**
public Integer findNodeIndex(int alignmentColumn)
{
Integer index;
- index = nodeLookup.get(alignmentColumn + 1);
+ index = nodeLookup.get(alignmentColumn);
return index;
}
}
}
- /**
- * Creates the HMM Logo alignment annotation, and populates it with
- * information content data.
- *
- * @return The alignment annotation.
- */
- public AlignmentAnnotation createAnnotation(int length)
- {
- Annotation[] annotations = new Annotation[length];
- float max = 0f;
- for (int alignPos = 0; alignPos < length; alignPos++)
- {
- Float content = getInformationContent(alignPos);
- if (content > max)
- {
- max = content;
- }
-
- Character cons;
-
- cons = getConsensusAtAlignColumn(alignPos);
-
- cons = Character.toUpperCase(cons);
-
- String description = String.format("%.3f", content);
- description += " bits";
- annotations[alignPos] = new Annotation(cons.toString(), description,
- ' ',
- content);
-
- }
- AlignmentAnnotation annotation = new AlignmentAnnotation(
- "Information",
- "The information content of each column, measured in bits",
- annotations,
- 0f, max, AlignmentAnnotation.BAR_GRAPH);
- annotation.setHMM(this);
- return annotation;
- }
-
- /**
- * Returns the information content at a specified column.
- *
- * @param column
- * Index of the column, starting from 0.
- * @return
- */
- public float getInformationContent(int column)
- {
- float informationContent = 0f;
-
- for (char symbol : symbols)
- {
- float freq = 0f;
- if ("amino".equals(getAlphabetType()))
- {
- freq = ResidueProperties.aminoBackgroundFrequencies.get(symbol);
- }
- if ("DNA".equals(getAlphabetType()))
- {
- freq = ResidueProperties.dnaBackgroundFrequencies.get(symbol);
- }
- if ("RNA".equals(getAlphabetType()))
- {
- freq = ResidueProperties.rnaBackgroundFrequencies
- .get(symbol);
- }
- Double hmmProb = getMatchEmissionProbability(column, symbol);
- float prob = hmmProb.floatValue();
- informationContent += prob * (Math.log(prob / freq) / Math.log(2));
- }
-
- return informationContent;
- }
/**
* Returns the consensus sequence based on the most probable symbol at each
* The length of the longest sequence in the existing alignment.
* @return
*/
- public Sequence getConsensusSequence(int length)
+ public Sequence getConsensusSequence()
{
int start;
int end;
start = getNodeAlignmentColumn(1);
modelLength = getLength();
end = getNodeAlignmentColumn(modelLength);
- char[] sequence = new char[length];
- for (int index = 0; index < length; index++)
+ char[] sequence = new char[end];
+ for (int index = 0; index < end; index++)
{
Character character;
}
- Sequence seq = new Sequence("HMM CONSENSUS", sequence, start, end);
+ Sequence seq = new Sequence(getName() + "_HMM", sequence, start, end);
return seq;
}
* Maps the nodes of the hidden Markov model to the reference annotation and
* then deletes this annotation.
*/
- public void mapToReferenceAnnotation(AlignFrame af)
+ public void mapToReferenceAnnotation(AlignFrame af, SequenceI seq)
{
AlignmentAnnotation annotArray[] = af.getViewport().getAlignment()
.getAlignmentAnnotation();
return;
}
+ mapToReferenceAnnotation(reference, seq);
+ af.getViewport().getAlignment().deleteAnnotation(reference);
+ }
+
+ public void mapToReferenceAnnotation(AlignmentAnnotation reference,
+ SequenceI seq)
+ {
+ HiddenMarkovModel hmm = seq.getHMM();
+ Annotation[] annots = reference.annotations;
+ {
+ int nodeIndex = 0;
+ for (int col = 0; col < annots.length; col++)
+ {
+ String character = annots[col].displayCharacter;
+ if ("x".equals(character) || "X".equals(character))
+ {
+ nodeIndex++;
+ if (nodeIndex < hmm.getNodes().size())
+ {
+ HMMNode node = hmm.getNode(nodeIndex);
+ int alignPos = getNodeAlignmentColumn(nodeIndex);
+ char seqCharacter = seq.getCharAt(alignPos);
+ if (alignPos >= seq.getLength() || col >= seq.getLength())
+ {
+ seq.insertCharAt(seq.getLength(),
+ (alignPos + 1) - seq.getLength(),
+ '-');
+ }
+ seq.getSequence()[alignPos] = '-';
+ seq.getSequence()[col] = seqCharacter;
+ node.setAlignmentColumn(col);
+ hmm.nodeLookup.put(col, nodeIndex);
+ }
+ else
+ {
+ System.out.println(
+ "The reference annotation contains more consensus columns than the hidden Markov model");
+ break;
+ }
+ }
+ else
+ {
+ hmm.nodeLookup.remove(col);
+ }
+ }
+
+ }
+
+ }
+
+ public void mapToReferenceAnnotation(AlignmentAnnotation reference)
+ {
Annotation[] annots = reference.annotations;
{
int nodeIndex = 0;
nodeIndex++;
if (nodeIndex < nodes.size())
{
- nodes.get(nodeIndex).setAlignmentColumn(col + 1);
- nodeLookup.put(col + 1, nodeIndex);
+ HMMNode node = nodes.get(nodeIndex);
+ node.setAlignmentColumn(col + 1);
+ nodeLookup.put(col, nodeIndex);
}
else
{
}
else
{
- nodeLookup.remove(col + 1);
+ nodeLookup.remove(col);
}
}
}
- af.getViewport().getAlignment().deleteAnnotation(reference);
+
}
- public void initPlaceholder(AlignFrame af)
+ public SequenceI initHMMSequence()
{
- AlignmentI alignment = af.getViewport().getAlignment();
- int length = alignment.getWidth();
- Sequence consensus = getConsensusSequence(length);
+ Sequence consensus = getConsensusSequence();
+ consensus.setIsHMMConsensusSequence(true);
consensus.setHMM(this);
- SequenceI[] consensusArr = new Sequence[] { consensus };
- AlignmentI newAlignment = new Alignment(consensusArr);
- newAlignment.append(alignment);
- af.getViewport().setAlignment(newAlignment);
+ return consensus;
}
+
}
git://source.jalview.org / jalview.git / blobdiff