import jalview.datamodel.SequenceI;
import jalview.renderer.ResidueShaderI;
import jalview.schemes.ColourSchemeI;
+import jalview.viewmodel.ViewportRanges;
import java.awt.Color;
import java.awt.Font;
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();
/**
boolean isIgnoreGapsConsensus();
+ boolean isIgnoreBelowBackground();
+
boolean isCalculationInProgress(AlignmentAnnotation alignmentAnnotation);
AlignmentAnnotation getAlignmentQualityAnnot();
AlignmentAnnotation getAlignmentConsensusAnnotation();
/**
+ * get the container for alignment gap annotation
+ *
+ * @return
+ */
+ AlignmentAnnotation getAlignmentGapAnnotation();
+
+ /**
* get the container for cDNA complement consensus annotation
*
* @return
* 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);
+
+ 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);
+
}