*
* @return
*/
- public ViewportRanges getRanges();
+ ViewportRanges getRanges();
/**
* calculate the height for visible annotation, revalidating bounds where
*
* @return total height of annotation
*/
- public int calcPanelHeight();
+ int calcPanelHeight();
/**
* Answers true if the viewport has at least one column selected
boolean isNormaliseSequenceLogo();
+ boolean isShowInformationHistogram();
+
+ boolean isShowHMMSequenceLogo();
+
+ boolean isNormaliseHMMSequenceLogo();
+
ColourSchemeI getGlobalColourScheme();
/**
boolean isIgnoreGapsConsensus();
+ boolean isIgnoreBelowBackground();
+
boolean isCalculationInProgress(AlignmentAnnotation alignmentAnnotation);
AlignmentAnnotation getAlignmentQualityAnnot();
*
* @return a copy of this view's current display settings
*/
- public ViewStyleI getViewStyle();
+ ViewStyleI getViewStyle();
/**
* update the view's display settings with the given style set
*
* @param settingsForView
*/
- public void setViewStyle(ViewStyleI settingsForView);
+ void setViewStyle(ViewStyleI settingsForView);
/**
* Returns a viewport which holds the cDna for this (protein), or vice versa,
*/
void setFollowHighlight(boolean b);
- public void applyFeaturesStyle(FeatureSettingsModelI featureSettings);
+ void applyFeaturesStyle(FeatureSettingsModelI featureSettings);
/**
* check if current selection group is defined on the view, or is simply a
@Override
void setProteinFontAsCdna(boolean b);
- public abstract TreeModel getCurrentTree();
+ void setSequenceInformationHashes(List<ProfilesI> info);
+
+ List<ProfilesI> getSequenceInformationHashes();
+
+ ProfilesI getSequenceInformationHash(int index);
+
+ List<AlignmentAnnotation> getInformationAnnotations();
+
+ AlignmentAnnotation getInformationAnnotation(int index);
+
+ void setSequenceInformationHash(ProfilesI info, int index);
+
+ /**
+ * Initiates the information annotation for all uninitiated sequences.
+ */
+ void initInformation();
+
+ /**
+ * Updates all information annotations.
+ *
+ * @param ap
+ */
+ void updateInformation(AlignmentViewPanel ap);
+
+ boolean isInfoLetterHeight();
+
+ abstract TreeModel getCurrentTree();
- public abstract void setCurrentTree(TreeModel tree);
+ abstract void setCurrentTree(TreeModel tree);
}