6 import java.util.Hashtable;
9 import jalview.datamodel.AlignmentAnnotation;
10 import jalview.datamodel.AlignmentI;
11 import jalview.datamodel.AnnotatedCollectionI;
12 import jalview.datamodel.ColumnSelection;
13 import jalview.datamodel.SequenceCollectionI;
14 import jalview.datamodel.SequenceI;
15 import jalview.schemes.ColourSchemeI;
16 import jalview.schemes.RNAHelicesColour;
22 public interface AlignViewportI
31 boolean hasHiddenColumns();
33 boolean isValidCharWidth();
35 boolean isShowConsensusHistogram();
37 boolean isShowSequenceLogo();
39 boolean isNormaliseSequenceLogo();
41 ColourSchemeI getGlobalColourScheme();
43 AlignmentI getAlignment();
45 ColumnSelection getColumnSelection();
47 Hashtable[] getSequenceConsensusHash();
49 Hashtable[] getRnaStructureConsensusHash();
51 boolean getIgnoreGapsConsensus();
53 boolean getCentreColumnLabels();
55 boolean isCalculationInProgress(AlignmentAnnotation alignmentAnnotation);
57 AlignmentAnnotation getAlignmentQualityAnnot();
59 AlignmentAnnotation getAlignmentConservationAnnotation();
61 * get the container for alignment consensus annotation
64 AlignmentAnnotation getAlignmentConsensusAnnotation();
67 * Test to see if viewport is still open and active
68 * @return true indicates that all references to viewport should be dropped
72 * get the associated calculation thread manager for the view
75 AlignCalcManagerI getCalcManager();
78 * get the percentage gaps allowed in a conservation calculation
81 public int getConsPercGaps();
84 * set the consensus result object for the viewport
87 void setSequenceConsensusHash(Hashtable[] hconsensus);
91 * @return the alignment annotatino row for the structure consensus calculation
93 AlignmentAnnotation getAlignmentStrucConsensusAnnotation();
96 * set the Rna structure consensus result object for the viewport
97 * @param hStrucConsensus
99 void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus);
102 * set global colourscheme
105 void setGlobalColourScheme(ColourSchemeI rhc);
107 Map<SequenceI, SequenceCollectionI> getHiddenRepSequences();
109 void setHiddenRepSequences(
110 Map<SequenceI, SequenceCollectionI> hiddenRepSequences);