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add partial button fix to annotation and statistics output
[jalview.git]
/
src
/
jalview
/
gui
/
AlignViewport.java
diff --git
a/src/jalview/gui/AlignViewport.java
b/src/jalview/gui/AlignViewport.java
index
86e1144
..
2005b91
100644
(file)
--- a/
src/jalview/gui/AlignViewport.java
+++ b/
src/jalview/gui/AlignViewport.java
@@
-652,10
+652,10
@@
public class AlignViewport extends AlignmentViewport implements
*/
public SequenceI[][] collateForPDB(PDBEntry[] pdbEntries)
{
*/
public SequenceI[][] collateForPDB(PDBEntry[] pdbEntries)
{
- List<SequenceI[]> seqvectors = new ArrayList<SequenceI[]>();
+ List<SequenceI[]> seqvectors = new ArrayList<>();
for (PDBEntry pdb : pdbEntries)
{
for (PDBEntry pdb : pdbEntries)
{
- List<SequenceI> choosenSeqs = new ArrayList<SequenceI>();
+ List<SequenceI> choosenSeqs = new ArrayList<>();
for (SequenceI sq : alignment.getSequences())
{
Vector<PDBEntry> pdbRefEntries = sq.getDatasetSequence()
for (SequenceI sq : alignment.getSequences())
{
Vector<PDBEntry> pdbRefEntries = sq.getDatasetSequence()
@@
-708,6
+708,11
@@
public class AlignViewport extends AlignmentViewport implements
normaliseSequenceLogo = state;
}
normaliseSequenceLogo = state;
}
+ public void setNormaliseHMMSequenceLogo(boolean state)
+ {
+ normaliseHMMSequenceLogo = state;
+ }
+
/**
*
* @return true if alignment characters should be displayed
/**
*
* @return true if alignment characters should be displayed
@@
-718,7
+723,7
@@
public class AlignViewport extends AlignmentViewport implements
return validCharWidth;
}
return validCharWidth;
}
- private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<String, AutoCalcSetting>();
+ private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<>();
public AutoCalcSetting getCalcIdSettingsFor(String calcId)
{
public AutoCalcSetting getCalcIdSettingsFor(String calcId)
{
@@
-1149,4
+1154,11
@@
public class AlignViewport extends AlignmentViewport implements
fr.setTransparency(featureSettings.getTransparency());
}
fr.setTransparency(featureSettings.getTransparency());
}
+ @Override
+ public boolean isNormaliseHMMSequenceLogo()
+ {
+ // TODO Auto-generated method stub
+ return normaliseHMMSequenceLogo;
+ }
+
}
}