JAL-2629 add documentation to previous work

[jalview.git] / src / jalview / workers / InformationThread.java

diff --git a/src/jalview/workers/InformationThread.java b/src/jalview/workers/InformationThread.java
index 67dd838..2c92879 100644 (file)
--- a/src/jalview/workers/InformationThread.java
+++ b/src/jalview/workers/InformationThread.java
@@ -15,7 +15,12 @@ import java.util.List;
 
 public class InformationThread extends AlignCalcWorker
 {
-
+  /**
+   * Constructor for information thread.
+   * 
+   * @param alignViewport
+   * @param alignPanel
+   */
   public InformationThread(AlignViewportI alignViewport,
             AlignmentViewPanel alignPanel)
     {
@@ -110,8 +115,10 @@ public class InformationThread extends AlignCalcWorker
 
 
     /**
-     * @param alignment
-     */
+   * Computes the profiles from a HMM for an alignment.
+   * 
+   * @param alignment
+   */
   protected void computeInformation(AlignmentI alignment)
     {
 
@@ -121,7 +128,7 @@ public class InformationThread extends AlignCalcWorker
     for (SequenceI seq : hmmSeqs)
     {
       HiddenMarkovModel hmm = seq.getHMM();
-      ProfilesI hinformation = AAFrequency.calculateInformation(hmm, width,
+      ProfilesI hinformation = AAFrequency.calculateHMMProfiles(hmm, width,
               0, width, true, alignViewport.isIgnoreBelowBackground());
       alignViewport.setSequenceInformationHash(hinformation, index);
       // setColourSchemeInformation(hinformation);
@@ -130,16 +137,15 @@ public class InformationThread extends AlignCalcWorker
     }
 
     /**
-     * @return
-     */
+   * gets the sequences on the alignment on the viewport.
+   * 
+   * @return
+   */
     protected SequenceI[] getSequences()
     {
       return alignViewport.getAlignment().getSequencesArray();
     }
 
-    /**
-   * @param hinformation
-   */
   protected void setColourSchemeInformation(ProfilesI information)
     {
       ResidueShaderI cs = alignViewport.getResidueShading();
@@ -180,7 +186,11 @@ public class InformationThread extends AlignCalcWorker
       updateResultAnnotation(false);
     }
 
-
+  /**
+   * Derives the information content for an information annotation.
+   * 
+   * @param immediate
+   */
     public void updateResultAnnotation(boolean immediate)
     {
     List<AlignmentAnnotation> annots = getInformationAnnotations();