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
JAL-2939 field/method naming more consistent
[jalview.git]
/
src
/
jalview
/
datamodel
/
SequenceGroup.java
diff --git
a/src/jalview/datamodel/SequenceGroup.java
b/src/jalview/datamodel/SequenceGroup.java
index
4c38aa0
..
aebcbb3
100755
(executable)
--- a/
src/jalview/datamodel/SequenceGroup.java
+++ b/
src/jalview/datamodel/SequenceGroup.java
@@
-134,7
+134,7
@@
public class SequenceGroup implements AnnotatedCollectionI
private boolean hmmUseInfoLetterHeight;
private boolean hmmUseInfoLetterHeight;
- private boolean showHMMSequenceLogo;
+ private boolean hmmShowSequenceLogo;
private boolean hmmNormaliseSequenceLogo;
private boolean hmmNormaliseSequenceLogo;
@@
-228,7
+228,7
@@
public class SequenceGroup implements AnnotatedCollectionI
showSequenceLogo = seqsel.showSequenceLogo;
normaliseSequenceLogo = seqsel.normaliseSequenceLogo;
showConsensusHistogram = seqsel.showConsensusHistogram;
showSequenceLogo = seqsel.showSequenceLogo;
normaliseSequenceLogo = seqsel.normaliseSequenceLogo;
showConsensusHistogram = seqsel.showConsensusHistogram;
- showHMMSequenceLogo = seqsel.showHMMSequenceLogo;
+ hmmShowSequenceLogo = seqsel.hmmShowSequenceLogo;
hmmNormaliseSequenceLogo = seqsel.hmmNormaliseSequenceLogo;
hmmShowHistogram = seqsel.hmmShowHistogram;
idColour = seqsel.idColour;
hmmNormaliseSequenceLogo = seqsel.hmmNormaliseSequenceLogo;
hmmShowHistogram = seqsel.hmmShowHistogram;
idColour = seqsel.idColour;
@@
-617,8
+617,7
@@
public class SequenceGroup implements AnnotatedCollectionI
ProfilesI info = AAFrequency.calculateHMMProfiles(hmm,
(endRes + 1) - startRes, startRes, endRes + 1,
ProfilesI info = AAFrequency.calculateHMMProfiles(hmm,
(endRes + 1) - startRes, startRes, endRes + 1,
- showHMMSequenceLogo, hmmIgnoreBelowBackground,
- hmmUseInfoLetterHeight);
+ hmmIgnoreBelowBackground, hmmUseInfoLetterHeight);
_updateInformationRow(info);
upd = true;
}
_updateInformationRow(info);
upd = true;
}
@@
-1579,18
+1578,16
@@
public class SequenceGroup implements AnnotatedCollectionI
// recalcConservation(); TODO don't know what to do here next
}
this.hmmShowHistogram = state;
// recalcConservation(); TODO don't know what to do here next
}
this.hmmShowHistogram = state;
-
}
public boolean isShowHMMSequenceLogo()
{
}
public boolean isShowHMMSequenceLogo()
{
- return showHMMSequenceLogo;
+ return hmmShowSequenceLogo;
}
}
- public void setshowHMMSequenceLogo(boolean state)
+ public void setShowHMMSequenceLogo(boolean state)
{
{
- showHMMSequenceLogo = state;
-
+ hmmShowSequenceLogo = state;
}
public boolean isNormaliseHMMSequenceLogo()
}
public boolean isNormaliseHMMSequenceLogo()
@@
-1600,7
+1597,7
@@
public class SequenceGroup implements AnnotatedCollectionI
public void setNormaliseHMMSequenceLogo(boolean state)
{
public void setNormaliseHMMSequenceLogo(boolean state)
{
- normaliseSequenceLogo = state;
+ hmmNormaliseSequenceLogo = state;
}
@Override
}
@Override