Merge branch 'features/mchmmer' into merge/wsinterfaces_mchmmer_JAL-3070_JAL-1950

[jalview.git] / src / jalview / schemes / HmmerGlobalBackground.java

diff --git a/src/jalview/schemes/HmmerGlobalBackground.java b/src/jalview/schemes/HmmerGlobalBackground.java
new file mode 100644 (file)
index 0000000..31bcadf
--- /dev/null
+++ b/src/jalview/schemes/HmmerGlobalBackground.java
@@ -0,0 +1,61 @@
+package jalview.schemes;
+
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+
+/**
+ * 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 sequence collection
+   * 
+   * @param ac
+   */
+  public HmmerGlobalBackground(SequenceCollectionI ac)
+  {
+    super(ac.getHmmSequences());
+    String alphabetType = getHmm() == null
+            ? ResidueProperties.ALPHABET_AMINO
+            : getHmm().getAlphabetType();
+    setFrequencies(
+            ResidueProperties.backgroundFrequencies.get(alphabetType));
+  }
+
+  /**
+   * Default constructor (required by ColourSchemes.loadColourSchemes)
+   */
+  public HmmerGlobalBackground()
+  {
+  }
+
+  @Override
+  public String getSchemeName()
+  {
+    return JalviewColourScheme.HMMERU.toString();
+  }
+
+  @Override
+  protected HmmerColourScheme newInstance(AnnotatedCollectionI ac)
+  {
+    return new HmmerGlobalBackground(ac);
+  }
+
+  @Override
+  float getMaxInformationScore()
+  {
+    return MAX_LOG_RATIO;
+  }
+
+}