return result;
}
+
/**
* Extract a sorted extract of cDNA codon profile data. The returned array
* contains
for (int col = 0; col < cols; col++)
{
// todo would prefer a Java bean for consensus data
- Hashtable<String, int[]> columnHash = new Hashtable<String, int[]>();
+ Hashtable<String, int[]> columnHash = new Hashtable<>();
// #seqs, #ungapped seqs, counts indexed by (codon encoded + 1)
int[] codonCounts = new int[66];
codonCounts[0] = alignment.getSequences().size();
Map<Character, Double> backgroundFrequencies = new HashMap();
+ ProfilesI profiles;
+
final static String YES = "yes";
return value;
}
- public char getConsensus(int columnIndex)
+ public char getConsensusAtAlignColumn(int columnIndex)
{
char value;
Integer index = findNodeIndex(columnIndex + 1);
{
Annotation[] annotations = new Annotation[length];
float max = 0f;
- for (int i = 0; i < length; i++)
+ for (int alignPos = 0; alignPos < length; alignPos++)
{
- Float content = getInformationContent(i);
+ 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[i] = new Annotation(null, description, ' ', content);
+ annotations[alignPos] = new Annotation(cons.toString(), description,
+ ' ',
+ content);
}
AlignmentAnnotation annotation = new AlignmentAnnotation(
return informationContent;
}
+
}
pop.add(item);
}
}
- else if (label.indexOf("Consensus") > -1)
+ else if (label.indexOf("Consensus") > -1
+ || label.indexOf("Information Content") > -1)
{
pop.addSeparator();
// av and sequencegroup need to implement same interface for
import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.HiddenMarkovModel;
import jalview.datamodel.ProfilesI;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.NucleotideColourScheme;
import jalview.schemes.ResidueProperties;
import jalview.schemes.ZappoColourScheme;
import jalview.util.Platform;
+import jalview.util.QuickSort;
import java.awt.BasicStroke;
import java.awt.Color;
import java.awt.image.ImageObserver;
import java.util.BitSet;
import java.util.Hashtable;
+import java.util.List;
public class AnnotationRenderer
{
private static final int CHAR_Z = 'Z'; // 90
+ private static final int AMINO = 0;
+
+ private static final int DNA = 1;
+
/**
* flag indicating if timing and redraw parameter info should be output
*/
av_ignoreGapsConsensus = av.isIgnoreGapsConsensus();
}
+ public int[] getHMMProfileFor(AlignmentAnnotation aa, int column,
+ boolean removeBelowBackground)
+ {
+
+ HiddenMarkovModel hmm;
+ hmm = aa.getHMM();
+ int size = 0;
+ int alphabet = 0;
+ String alph = hmm.getAlphabetType();
+ if (alph.equals("amino"))
+ {
+ size = 20;
+ alphabet = AMINO;
+ }
+ else if (alph.equals("DNA"))
+ {
+ size = 4;
+ alphabet = DNA;
+ }
+
+ char symbols[] = new char[size];
+ int values[] = new int[size];
+
+ List<Character> charList = hmm.getSymbols();
+
+ int i = 0;
+ for (char character : charList)
+ {
+ symbols[i] = character;
+ i++;
+ }
+
+ Integer totalCount = 0;
+ for (int j = 0; j < size; j++)
+ {
+ Double value;
+ char symbol = symbols[j];
+ value = hmm.getMatchEmissionProbability(column, symbol);
+ double freq;
+
+ if (alphabet == AMINO && removeBelowBackground)
+ {
+ freq = ResidueProperties.aminoBackgroundFrequencies.get(symbol);
+ if (value < freq)
+ {
+ value = 0d;
+ }
+ }
+ else if (alphabet == DNA && removeBelowBackground)
+ {
+ freq = ResidueProperties.nucleotideBackgroundFrequencies
+ .get(symbol);
+ if (value < freq)
+ {
+ value = 0d;
+ }
+ }
+ value = value * 10000;
+ values[j] = value.intValue();
+ totalCount += value.intValue();
+ }
+
+ QuickSort.sort(values, symbols);
+
+ int[] profile = new int[3 + size * 2];
+
+ profile[0] = AlignmentAnnotation.SEQUENCE_PROFILE;
+ profile[1] = size;
+ profile[2] = totalCount;
+
+ if (totalCount != 0)
+ {
+ int arrayPos = 3;
+ for (int k = size - 1; k >= 0; k--)
+ {
+ Double percentage;
+ Integer value = values[k];
+ percentage = (value.doubleValue() / totalCount.doubleValue())
+ * 100d;
+ profile[arrayPos] = symbols[k];
+ profile[arrayPos + 1] = percentage.intValue();
+ arrayPos += 2;
+ }
+ }
+
+ return profile;
+
+ }
+
/**
* Returns profile data; the first element is the profile type, the second is
* the number of distinct values, the third the total count, and the remainder
// properties/rendering attributes as a global 'alignment group' which holds
// all vis settings for the alignment as a whole rather than a subset
//
+ if (aa.label.startsWith("Information"))
+ {
+ return getHMMProfileFor(aa, column, true);
+ }
if (aa.autoCalculated
&& (aa.label.startsWith("Consensus") || aa.label
.startsWith("cDNA Consensus")))
package jalview.schemes;
+import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.HiddenMarkovModel;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
+import jalview.util.ColorUtils;
+import jalview.util.Comparison;
import java.awt.Color;
import java.util.Map;
{
if (hmm ==null)
{
- return new Color(255, 255, 255);
+ return Color.white;
}
return findColour(symbol, position);
}
public Color findColour(char symbol, int position)
{
+ if (Comparison.isGap(symbol))
+ {
+ return Color.white;
+ }
+ Double prob;
+ prob = hmm.getMatchEmissionProbability(position, symbol);
+ double freq = ResidueProperties.aminoBackgroundFrequencies.get(symbol);
+ Double value = prob - freq;
- Double probability;
- probability = hmm.getMatchEmissionProbability(position, symbol);
- // Double redModifier = Math.pow(probability, 0.9);
- Double doubleGreenModifier;
- float greenModifier;
- if (probability < 0.5)
+ Color colour = null;
+ if (value >= 0)
{
- doubleGreenModifier = probability;
- greenModifier = doubleGreenModifier.floatValue();
+
+ colour = ColorUtils.getGraduatedColour(value.floatValue(), 0,
+ Color.WHITE, 1f, Color.green);
}
- else
+ else if (value < 0)
{
- doubleGreenModifier = Math.pow(probability, 1 / 1.9);
- greenModifier = doubleGreenModifier.floatValue();
+ return Color.YELLOW;
+
}
- // Double blueModifier = Math.pow(probability, 0.9);
- return new Color(1f, 1f - greenModifier, 0.f);
+ return colour;
}
+
+
+
+
+
@Override
public void alignmentChanged(AnnotatedCollectionI collection,
Map<SequenceI, SequenceCollectionI> hiddenReps)
{
+ AlignmentAnnotation[] annArr = collection.getAlignmentAnnotation();
+ for (AlignmentAnnotation ann : annArr)
+ {
+ if (ann.label.indexOf("Information Content") > -1)
+ {
+ hmm = ann.getHMM();
+ }
+ }
- collection.setHMM(hmm);
}
@Override
public ColourSchemeI getInstance(AnnotatedCollectionI sg,
Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
{
+ HiddenMarkovModel markov = null;
+ AlignmentAnnotation[] annArr = sg.getAlignmentAnnotation();
+ for (AlignmentAnnotation ann : annArr)
+ {
+ if (ann.label.indexOf("Information Content") > -1)
+ {
+ markov = ann.getHMM();
+ }
+ }
- HMMERColourScheme markov = new HMMERColourScheme(sg.getHMM());
- return markov;
+ HMMERColourScheme colour = new HMMERColourScheme(markov);
+ return colour;
+
}
@Override
git://source.jalview.org / jalview.git / commitdiff