git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
add partial button fix to annotation and statistics output
[jalview.git]
/
src
/
jalview
/
api
/
AlignViewportI.java
diff --git
a/src/jalview/api/AlignViewportI.java
b/src/jalview/api/AlignViewportI.java
index
9e6d1c0
..
6ebde3c
100644
(file)
--- a/
src/jalview/api/AlignViewportI.java
+++ b/
src/jalview/api/AlignViewportI.java
@@
-86,6
+86,12
@@
public interface AlignViewportI extends ViewStyleI
boolean isNormaliseSequenceLogo();
boolean isNormaliseSequenceLogo();
+ boolean isShowInformationHistogram();
+
+ boolean isShowHMMSequenceLogo();
+
+ boolean isNormaliseHMMSequenceLogo();
+
ColourSchemeI getGlobalColourScheme();
/**
ColourSchemeI getGlobalColourScheme();
/**
@@
-113,6
+119,8
@@
public interface AlignViewportI extends ViewStyleI
boolean isIgnoreGapsConsensus();
boolean isIgnoreGapsConsensus();
+ boolean isIgnoreBelowBackground();
+
boolean isCalculationInProgress(AlignmentAnnotation alignmentAnnotation);
AlignmentAnnotation getAlignmentQualityAnnot();
boolean isCalculationInProgress(AlignmentAnnotation alignmentAnnotation);
AlignmentAnnotation getAlignmentQualityAnnot();
@@
-127,6
+135,13
@@
public interface AlignViewportI extends ViewStyleI
AlignmentAnnotation getAlignmentConsensusAnnotation();
/**
AlignmentAnnotation getAlignmentConsensusAnnotation();
/**
+ * get the container for alignment information content annotation
+ *
+ * @return
+ */
+ AlignmentAnnotation getAlignmentInformationAnnotation();
+
+ /**
* get the container for alignment gap annotation
*
* @return
* get the container for alignment gap annotation
*
* @return
@@
-486,6
+501,7
@@
public interface AlignViewportI extends ViewStyleI
*
* @return
*/
*
* @return
*/
+ @Override
boolean isProteinFontAsCdna();
/**
boolean isProteinFontAsCdna();
/**
@@
-493,5
+509,6
@@
public interface AlignViewportI extends ViewStyleI
*
* @return
*/
*
* @return
*/
+ @Override
void setProteinFontAsCdna(boolean b);
}
void setProteinFontAsCdna(boolean b);
}