6 import java.util.Hashtable;
8 import jalview.datamodel.AlignmentAnnotation;
9 import jalview.datamodel.AlignmentI;
10 import jalview.datamodel.ColumnSelection;
11 import jalview.schemes.ColourSchemeI;
12 import jalview.schemes.RNAHelicesColour;
18 public interface AlignViewportI
27 boolean hasHiddenColumns();
29 boolean isValidCharWidth();
31 boolean isShowConsensusHistogram();
33 boolean isShowSequenceLogo();
35 boolean isNormaliseSequenceLogo();
37 ColourSchemeI getGlobalColourScheme();
39 AlignmentI getAlignment();
41 ColumnSelection getColumnSelection();
43 Hashtable[] getSequenceConsensusHash();
45 Hashtable[] getRnaStructureConsensusHash();
47 boolean getIgnoreGapsConsensus();
49 boolean getCentreColumnLabels();
51 boolean isCalculationInProgress(AlignmentAnnotation alignmentAnnotation);
53 AlignmentAnnotation getAlignmentQualityAnnot();
55 AlignmentAnnotation getAlignmentConservationAnnotation();
57 * get the container for alignment consensus annotation
60 AlignmentAnnotation getAlignmentConsensusAnnotation();
63 * Test to see if viewport is still open and active
64 * @return true indicates that all references to viewport should be dropped
68 * get the associated calculation thread manager for the view
71 AlignCalcManagerI getCalcManager();
74 * get the percentage gaps allowed in a conservation calculation
77 public int getConsPercGaps();
80 * set the consensus result object for the viewport
83 void setSequenceConsensusHash(Hashtable[] hconsensus);
87 * @return the alignment annotatino row for the structure consensus calculation
89 AlignmentAnnotation getAlignmentStrucConsensusAnnotation();
92 * set the Rna structure consensus result object for the viewport
93 * @param hStrucConsensus
95 void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus);
98 * set global colourscheme
101 void setGlobalColourScheme(ColourSchemeI rhc);