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
32 * calculate the height for visible annotation, revalidating bounds where
33 * necessary ABSTRACT GUI METHOD
35 * @return total height of annotation
37 public int calcPanelHeight();
39 boolean hasHiddenColumns();
41 boolean isValidCharWidth();
43 boolean isShowConsensusHistogram();
45 boolean isShowSequenceLogo();
47 boolean isNormaliseSequenceLogo();
49 ColourSchemeI getGlobalColourScheme();
51 AlignmentI getAlignment();
53 ColumnSelection getColumnSelection();
55 Hashtable[] getSequenceConsensusHash();
57 Hashtable[] getRnaStructureConsensusHash();
59 boolean getIgnoreGapsConsensus();
61 boolean getCentreColumnLabels();
63 boolean isCalculationInProgress(AlignmentAnnotation alignmentAnnotation);
65 AlignmentAnnotation getAlignmentQualityAnnot();
67 AlignmentAnnotation getAlignmentConservationAnnotation();
70 * get the container for alignment consensus annotation
74 AlignmentAnnotation getAlignmentConsensusAnnotation();
77 * Test to see if viewport is still open and active
79 * @return true indicates that all references to viewport should be dropped
84 * get the associated calculation thread manager for the view
88 AlignCalcManagerI getCalcManager();
91 * get the percentage gaps allowed in a conservation calculation
94 public int getConsPercGaps();
97 * set the consensus result object for the viewport
101 void setSequenceConsensusHash(Hashtable[] hconsensus);
105 * @return the alignment annotatino row for the structure consensus
108 AlignmentAnnotation getAlignmentStrucConsensusAnnotation();
111 * set the Rna structure consensus result object for the viewport
113 * @param hStrucConsensus
115 void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus);
118 * set global colourscheme
122 void setGlobalColourScheme(ColourSchemeI rhc);
124 Map<SequenceI, SequenceCollectionI> getHiddenRepSequences();
126 void setHiddenRepSequences(
127 Map<SequenceI, SequenceCollectionI> hiddenRepSequences);
130 * hides or shows dynamic annotation rows based on groups and group and
131 * alignment associated auto-annotation state flags apply the current
132 * group/autoannotation settings to the alignment view. Usually you should
133 * call the AlignmentViewPanel.adjustAnnotationHeight() method afterwards to
134 * ensure the annotation panel bounds are set correctly.
136 * @param applyGlobalSettings
137 * - apply to all autoannotation rows or just the ones associated
138 * with the current visible region
139 * @param preserveNewGroupSettings
140 * - don't apply global settings to groups which don't already have
141 * group associated annotation
143 void updateGroupAnnotationSettings(boolean applyGlobalSettings,
144 boolean preserveNewGroupSettings);