import jalview.datamodel.SequenceI;
import jalview.renderer.ResidueShaderI;
import jalview.schemes.ColourSchemeI;
+import jalview.viewmodel.ViewportRanges;
import java.awt.Color;
+import java.awt.Font;
import java.util.Hashtable;
import java.util.List;
import java.util.Map;
public interface AlignViewportI extends ViewStyleI
{
- int getEndRes();
+ /**
+ * Get the ranges object containing details of the start and end sequences and
+ * residues
+ *
+ * @return
+ */
+ public ViewportRanges getRanges();
/**
* calculate the height for visible annotation, revalidating bounds where
boolean isNormaliseSequenceLogo();
+ boolean isShowInformationHistogram();
+
+ boolean isShowHMMSequenceLogo();
+
+ boolean isNormaliseHMMSequenceLogo();
+
ColourSchemeI getGlobalColourScheme();
/**
ProfilesI getSequenceConsensusHash();
+ ProfilesI getSequenceInformationHash();
+
/**
* Get consensus data table for the cDNA complement of this alignment (if any)
*
boolean isIgnoreGapsConsensus();
+ boolean isIgnoreBelowBackground();
+
boolean isCalculationInProgress(AlignmentAnnotation alignmentAnnotation);
AlignmentAnnotation getAlignmentQualityAnnot();
AlignmentAnnotation getAlignmentConsensusAnnotation();
/**
+ * get the container for alignment information content annotation
+ *
+ * @return
+ */
+ AlignmentAnnotation getAlignmentInformationAnnotation();
+
+ /**
* get the container for alignment gap annotation
*
* @return
void setSequenceConsensusHash(ProfilesI hconsensus);
/**
+ * set the information result object for the viewport
+ *
+ * @param hconsensus
+ */
+ void setSequenceInformationHash(ProfilesI hinformation);
+
+ /**
* Set the cDNA complement consensus for the viewport
*
* @param hconsensus
* @return search results or null
*/
SearchResultsI getSearchResults();
+
+ /**
+ * Updates view settings with the given font. You may need to call
+ * AlignmentPanel.fontChanged to update the layout geometry.
+ *
+ * @param setGrid
+ * when true, charWidth/height is set according to font metrics
+ */
+ void setFont(Font newFont, boolean b);
+
+ /**
+ * Answers true if split screen protein and cDNA use the same font
+ *
+ * @return
+ */
+ @Override
+ boolean isProteinFontAsCdna();
+
+ /**
+ * Set the flag for whether split screen protein and cDNA use the same font
+ *
+ * @return
+ */
+ @Override
+ void setProteinFontAsCdna(boolean b);
+
+ ProfilesI setSequenceInformationHash();
}