+++ /dev/null
-package jalview.schemes;
-
-import jalview.datamodel.AnnotatedCollectionI;
-import jalview.datamodel.HiddenMarkovModel;
-import jalview.datamodel.ResidueCount;
-import jalview.datamodel.SequenceCollectionI;
-import jalview.datamodel.SequenceI;
-import jalview.util.ColorUtils;
-import jalview.util.Comparison;
-
-import java.awt.Color;
-import java.util.HashMap;
-import java.util.Map;
-
-/**
- * A colour scheme based on a selected Hidden Markov Model. The colour is
- * <ul>
- * <li>white for a gap</li>
- * <li>red for an insertion</li>
- * <li>orange for negative information content</li>
- * <li>white to blue for increasing information content</li>
- * </ul>
- * where information content is the log ratio
- *
- * <pre>
- * log(profile match emission probability / residue background probability>
- * </pre>
- *
- * using the alignment's background frequencies for residues.
- *
- * @author tzvanaalten
- *
- */
-public class HMMERAlignmentColourScheme extends ResidueColourScheme
-{
- /*
- * the ratio, for each symbol, of its frequency to total symbol count
- */
- Map<Character, Double> frequency = new HashMap<>();
-
- float logTotalCount;
-
- HiddenMarkovModel hmm;
-
- /**
- * Constructor given a Hidden Markov Model
- *
- * @param sg
- *
- * @param markov
- */
- public HMMERAlignmentColourScheme(AnnotatedCollectionI sg,
- HiddenMarkovModel markov)
- {
- hmm = markov;
- countFrequencies(sg);
- }
-
- /**
- * Default constructor (required by ColourSchemes.loadColourSchemes)
- */
- public HMMERAlignmentColourScheme()
- {
- }
-
- @Override
- public Color findColour(char symbol, int position, SequenceI seq,
- String consensusResidue, float pid)
- {
- return findColour(symbol, position);
- }
-
- /**
- * Returns the colour at a particular symbol at a column in the alignment:
- * <ul>
- * <li>white for a gap</li>
- * <li>red for an insertion</li>
- * <li>orange for negative information content</li>
- * <li>white to blue for increasing information content</li>
- * </ul>
- *
- * @param symbol
- * @param column
- * @return
- */
- private Color findColour(char symbol, int column)
- {
- if (hmm == null || Comparison.isGap(symbol))
- {
- return Color.white;
- }
- if (Character.isLowerCase(symbol))
- {
- symbol = Character.toUpperCase(symbol);
- }
- double prob = hmm.getMatchEmissionProbability(column, symbol);
- Double freq = frequency.get(symbol);
- if (freq == null)
- {
- return Color.white;
- }
- if (prob == 0)
- {
- return new Color(230, 0, 0);
- }
- double value = Math.log(prob / freq.doubleValue());
- Color colour = null;
- if (value > 0)
- {
- colour = ColorUtils.getGraduatedColour((float) value, 0,
- Color.WHITE, logTotalCount, Color.blue);
- }
- else if (value < 0)
- {
- return Color.ORANGE;
- }
- return colour;
- }
-
- @Override
- public void alignmentChanged(AnnotatedCollectionI collection,
- Map<SequenceI, SequenceCollectionI> hiddenReps)
- {
- /*
- * ? no need to do anything if alignment is adjusted
- * since findColour() handles everything
- */
- }
-
- @Override
- public ColourSchemeI getInstance(AnnotatedCollectionI sg,
- Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
- {
- SequenceI hmmSeq = sg.getHmmConsensus();
- HiddenMarkovModel model = hmmSeq == null ? null : hmmSeq.getHMM();
- return new HMMERAlignmentColourScheme(sg, model);
- }
-
- /**
- * Answers true if the sequence collection has an HMM consensus sequence, else
- * false
- */
- @Override
- public boolean isApplicableTo(AnnotatedCollectionI ac)
- {
- return ac.getHmmConsensus() != null;
- }
-
- @Override
- public String getSchemeName()
- {
- return JalviewColourScheme.HMMERA.toString();
- }
-
- @Override
- public boolean isSimple()
- {
- return false;
- }
-
- /**
- * Counts and stores the relatively frequency of every residue in the
- * alignment
- *
- * @param sg
- */
- public void countFrequencies(AnnotatedCollectionI sg)
- {
- ResidueCount counts = new ResidueCount(sg.getSequences());
- int total = counts.getTotalResidueCount(); // excludes gaps
-
- for (char symbol : counts.getSymbolCounts().symbols)
- {
- double freq = counts.getCount(symbol) / (double) total;
- frequency.put(symbol, freq);
- }
- logTotalCount = (float) Math.log(total);
- }
-}
import java.util.Map;
/**
- * A colour scheme based on a selected Hidden Markov Model. The colour is
+ * Base class for colour schemes based on a selected Hidden Markov Model. The
+ * colour is
* <ul>
* <li>white for a gap</li>
* <li>red for an insertion</li>
* where information content is the log ratio
*
* <pre>
- * log(profile match emission probability / residue background probability>
+ * log(profile match emission probability / residue background probability)
* </pre>
*
- * using global ('Uniprot') background frequencies for residues.
+ * Sub-class implementations use either global ('Uniprot') or local
+ * ('alignment') background frequencies.
*
* @author tzvanaalten
- *
+ * @author gmcarstairs
*/
-public class HMMERColourScheme extends ResidueColourScheme
+public abstract class HmmerColourScheme extends ResidueColourScheme
{
- /*
- * The highest possible log ratio is when match emission probability in
- * the HMM model is 1, and background (for W) is 0.0109 giving
- * log(1/0.0109) = log(91.743) = 4.519
- */
- private static final float MAX_LOG_RATIO = 4.519f;
+ private static final Color INSERTION_COLOUR = new Color(230, 0, 0); // reddish
- private static final Color REDDISH = new Color(230, 0, 0);
+ private HiddenMarkovModel hmm;
- HiddenMarkovModel hmm;
+ private Map<Character, Float> frequencies;
/**
* Constructor given a Hidden Markov Model
*
* @param markov
*/
- public HMMERColourScheme(HiddenMarkovModel markov)
+ public HmmerColourScheme(HiddenMarkovModel markov)
{
hmm = markov;
}
/**
* Default constructor (required by ColourSchemes.loadColourSchemes)
*/
- public HMMERColourScheme()
+ public HmmerColourScheme()
{
}
*/
private Color findColour(char symbol, int column)
{
- if (hmm == null || Comparison.isGap(symbol))
+ if (getHmm() == null || Comparison.isGap(symbol))
{
return Color.white;
}
symbol = Character.toUpperCase(symbol);
}
- double prob = hmm.getMatchEmissionProbability(column, symbol);
+ double prob = getHmm().getMatchEmissionProbability(column, symbol);
Float freq = 0f;
- String alpha = hmm.getAlphabetType();
- if (!ResidueProperties.backgroundFrequencies.get(alpha)
- .containsKey(symbol))
+
+ if (!frequencies.containsKey(symbol))
{
return Color.WHITE;
}
else
{
- freq = ResidueProperties.backgroundFrequencies.get(alpha).get(symbol);
+ freq = frequencies.get(symbol);
}
if (prob == 0D)
{
- return REDDISH;
+ return INSERTION_COLOUR;
}
double value = Math.log(prob / freq.floatValue());
Color colour = null;
if (value > 0)
{
colour = ColorUtils.getGraduatedColour((float) value, 0,
- Color.WHITE, MAX_LOG_RATIO, Color.blue);
+ Color.WHITE, getMaxInformationScore(), Color.blue);
}
else if (value < 0)
{
return colour;
}
+ /**
+ * Answers the maximum possible value of information score (log ratio), for
+ * use in scaling a graduated colour range
+ *
+ * @return
+ */
+ abstract float getMaxInformationScore();
+
@Override
public void alignmentChanged(AnnotatedCollectionI collection,
Map<SequenceI, SequenceCollectionI> hiddenReps)
/**
* Answers a new colour scheme instance based on the HMM of the first sequence
- * in sg that has an HMM
+ * in ac that has an HMM
*/
@Override
- public ColourSchemeI getInstance(AnnotatedCollectionI sg,
+ public ColourSchemeI getInstance(AnnotatedCollectionI ac,
Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
{
- SequenceI hmmSeq = sg.getHmmConsensus();
+ SequenceI hmmSeq = ac.getHmmConsensus();
HiddenMarkovModel model = hmmSeq == null ? null : hmmSeq.getHMM();
- HMMERColourScheme colour = new HMMERColourScheme(model);
- return colour;
+ return newInstance(ac, model);
}
- @Override
- public String getSchemeName()
- {
- return JalviewColourScheme.HMMERU.toString();
- }
+ /**
+ * Answers a new instance of the colour scheme for the given HMM
+ *
+ * @param ac
+ * @param model
+ * @return
+ */
+ protected abstract HmmerColourScheme newInstance(AnnotatedCollectionI ac,
+ HiddenMarkovModel model);
@Override
public boolean isSimple()
return ac.getHmmConsensus() != null;
}
+ protected Map<Character, Float> getFrequencies()
+ {
+ return frequencies;
+ }
+
+ protected void setFrequencies(Map<Character, Float> frequencies)
+ {
+ this.frequencies = frequencies;
+ }
+
+ protected HiddenMarkovModel getHmm()
+ {
+ return hmm;
+ }
+
}
--- /dev/null
+package jalview.schemes;
+
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.HiddenMarkovModel;
+
+/**
+ * An HMM colour scheme that uses global ('Uniprot') background frequencies for
+ * residues
+ *
+ * @author tzvanaalten
+ */
+public class HmmerGlobalBackground extends HmmerColourScheme
+{
+ /*
+ * The highest possible log ratio is when match emission probability in
+ * the HMM model is 1, and background (for W) is 0.0109 giving
+ * log(1/0.0109) = log(91.743) = 4.519
+ */
+ private static final float MAX_LOG_RATIO = 4.519f;
+
+ /**
+ * Constructor given a Hidden Markov Model
+ *
+ * @param markov
+ */
+ public HmmerGlobalBackground(HiddenMarkovModel markov)
+ {
+ super(markov);
+ setFrequencies(ResidueProperties.backgroundFrequencies
+ .get(getHmm().getAlphabetType()));
+ }
+
+ /**
+ * Default constructor (required by ColourSchemes.loadColourSchemes)
+ */
+ public HmmerGlobalBackground()
+ {
+ }
+
+ @Override
+ public String getSchemeName()
+ {
+ return JalviewColourScheme.HMMERU.toString();
+ }
+
+ @Override
+ protected HmmerColourScheme newInstance(AnnotatedCollectionI ac,
+ HiddenMarkovModel model)
+ {
+ return new HmmerGlobalBackground(model);
+ }
+
+ @Override
+ float getMaxInformationScore()
+ {
+ return MAX_LOG_RATIO;
+ }
+
+}
--- /dev/null
+package jalview.schemes;
+
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.HiddenMarkovModel;
+import jalview.datamodel.ResidueCount;
+
+import java.util.HashMap;
+import java.util.Map;
+
+/**
+ * An HMM colour scheme that uses local (alignment or sub-group) background
+ * frequencies for residues
+ *
+ * @author tzvanaalten
+ */
+public class HmmerLocalBackground extends HmmerColourScheme
+{
+ float logTotalCount;
+
+ /**
+ * Constructor given a Hidden Markov Model
+ *
+ * @param sg
+ *
+ * @param markov
+ */
+ public HmmerLocalBackground(AnnotatedCollectionI sg,
+ HiddenMarkovModel markov)
+ {
+ super(markov);
+ countFrequencies(sg);
+ }
+
+ /**
+ * Default constructor (required by ColourSchemes.loadColourSchemes)
+ */
+ public HmmerLocalBackground()
+ {
+ }
+
+ @Override
+ public String getSchemeName()
+ {
+ return JalviewColourScheme.HMMERA.toString();
+ }
+
+ /**
+ * Counts and stores the relative frequency of every residue in the alignment
+ *
+ * @param sg
+ */
+ public void countFrequencies(AnnotatedCollectionI sg)
+ {
+ Map<Character, Float> freqs = new HashMap<>();
+ ResidueCount counts = new ResidueCount(sg.getSequences());
+ int total = counts.getTotalResidueCount(); // excludes gaps
+
+ for (char symbol : counts.getSymbolCounts().symbols)
+ {
+ double freq = counts.getCount(symbol) / (double) total;
+ freqs.put(symbol, (float) freq);
+ }
+
+ setFrequencies(freqs);
+
+ logTotalCount = (float) Math.log(total);
+ }
+
+ @Override
+ float getMaxInformationScore()
+ {
+ return logTotalCount;
+ }
+
+ @Override
+ protected HmmerColourScheme newInstance(AnnotatedCollectionI ac,
+ HiddenMarkovModel model)
+ {
+ return new HmmerLocalBackground(ac, model);
+ }
+}
PurinePyrimidine("Purine/Pyrimidine", PurinePyrimidineColourScheme.class),
RNAHelices("RNA Helices", RNAHelicesColour.class),
TCoffee("T-Coffee Scores", TCoffeeColourScheme.class),
- HMMERU("HMMER-Uniprot", HMMERColourScheme.class),
- HMMERA("HMMER-Alignment", HMMERAlignmentColourScheme.class);
+ HMMERU("HMMER-Uniprot", HmmerColourScheme.class),
+ HMMERA("HMMER-Alignment", HmmerLocalBackground.class);
// RNAInteraction("RNA Interaction type", RNAInteractionColourScheme.class)
private String name;
import org.testng.annotations.Test;
-public class HMMERColourSchemeTest {
+public class HmmerGlobalBackgroundTest {
@Test(groups = "Functional")
public void testFindColour() throws MalformedURLException, IOException
HMMFile file = new HMMFile("test/jalview/io/test_PKinase_hmm.txt",
DataSourceType.FILE);
- ColourSchemeI scheme = new HMMERColourScheme(file.getHMM());
+ ColourSchemeI scheme = new HmmerGlobalBackground(file.getHMM());
/*
* 'A' in column 1, node 2, match emission 2.77204
import org.testng.annotations.Test;
-public class HMMERAlignmentColourSchemeTest {
+public class HmmerLocalBackgroundTest {
@Test(groups = "Functional")
public void testFindColour() throws MalformedURLException, IOException
SequenceI seq1 = new Sequence("seq1", "AAMMMKKKVV");
SequenceI seq2 = new Sequence("seq2", "aAM-QKRSSSL");
AnnotatedCollectionI ac = new Alignment(new SequenceI[] { seq1, seq2 });
- ColourSchemeI scheme = new HMMERAlignmentColourScheme(ac,
+ ColourSchemeI scheme = new HmmerLocalBackground(ac,
file.getHMM());
/*
git://source.jalview.org / jalview.git / commitdiff