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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
ad6731a
..
2005b91
100644
(file)
--- a/
src/jalview/gui/AlignViewport.java
+++ b/
src/jalview/gui/AlignViewport.java
@@
-57,6
+57,7
@@
import jalview.ws.params.AutoCalcSetting;
import java.awt.Container;
import java.awt.Dimension;
import java.awt.Font;
import java.awt.Container;
import java.awt.Dimension;
import java.awt.Font;
+import java.awt.FontMetrics;
import java.awt.Rectangle;
import java.util.ArrayList;
import java.util.Hashtable;
import java.awt.Rectangle;
import java.util.ArrayList;
import java.util.Hashtable;
@@
-351,23
+352,19
@@
public class AlignViewport extends AlignmentViewport implements
boolean validCharWidth;
/**
boolean validCharWidth;
/**
- * update view settings with the given font. You may need to call
- * alignPanel.fontChanged to update the layout geometry
- *
- * @param setGrid
- * when true, charWidth/height is set according to font mentrics
+ * {@inheritDoc}
*/
*/
+ @Override
public void setFont(Font f, boolean setGrid)
{
font = f;
Container c = new Container();
public void setFont(Font f, boolean setGrid)
{
font = f;
Container c = new Container();
- java.awt.FontMetrics fm = c.getFontMetrics(font);
- int w = viewStyle.getCharWidth(), ww = fm.charWidth('M'), h = viewStyle
- .getCharHeight();
if (setGrid)
{
if (setGrid)
{
+ FontMetrics fm = c.getFontMetrics(font);
+ int ww = fm.charWidth('M');
setCharHeight(fm.getHeight());
setCharWidth(ww);
}
setCharHeight(fm.getHeight());
setCharWidth(ww);
}
@@
-655,10
+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()
@@
-711,6
+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
@@
-721,7
+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)
{
@@
-1052,8
+1054,9
@@
public class AlignViewport extends AlignmentViewport implements
// TODO would like next line without cast but needs more refactoring...
final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement())
.getAlignPanel();
// TODO would like next line without cast but needs more refactoring...
final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement())
.getAlignPanel();
- complementPanel.setDontScrollComplement(true);
+ complementPanel.setToScrollComplementPanel(false);
complementPanel.scrollToCentre(sr, verticalOffset);
complementPanel.scrollToCentre(sr, verticalOffset);
+ complementPanel.setToScrollComplementPanel(true);
}
}
}
}
@@
-1151,4
+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;
+ }
+
}
}