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JAL-2629 can now filter by sequence e-value or bit score
[jalview.git]
/
src
/
jalview
/
appletgui
/
AlignViewport.java
diff --git
a/src/jalview/appletgui/AlignViewport.java
b/src/jalview/appletgui/AlignViewport.java
index
7ce6837
..
edacce8
100644
(file)
--- a/
src/jalview/appletgui/AlignViewport.java
+++ b/
src/jalview/appletgui/AlignViewport.java
@@
-79,7
+79,7
@@
public class AlignViewport extends AlignmentViewport
{
try
{
{
try
{
- widthScale = new Float(param).floatValue();
+ widthScale = Float.valueOf(param).floatValue();
} catch (Exception e)
{
}
} catch (Exception e)
{
}
@@
-102,7
+102,7
@@
public class AlignViewport extends AlignmentViewport
{
try
{
{
try
{
- heightScale = new Float(param).floatValue();
+ heightScale = Float.valueOf(param).floatValue();
} catch (Exception e)
{
}
} catch (Exception e)
{
}
@@
-203,11
+203,11
@@
public class AlignViewport extends AlignmentViewport
if (colour != null)
{
residueShading = new ResidueShader(
if (colour != null)
{
residueShading = new ResidueShader(
- ColourSchemeProperty.getColourScheme(getAlignment(),
+ ColourSchemeProperty.getColourScheme(this, alignment,
colour));
if (residueShading != null)
{
colour));
if (residueShading != null)
{
- residueShading.setConsensus(hconsensus);
+ residueShading.setConsensus(consensusProfiles);
}
}
}
}
@@
-299,17
+299,6
@@
public class AlignViewport extends AlignmentViewport
.getStructureSelectionManager(applet);
}
.getStructureSelectionManager(applet);
}
- @Override
- public boolean isNormaliseSequenceLogo()
- {
- return normaliseSequenceLogo;
- }
-
- public void setNormaliseSequenceLogo(boolean state)
- {
- normaliseSequenceLogo = state;
- }
-
/**
*
* @return true if alignment characters should be displayed
/**
*
* @return true if alignment characters should be displayed
@@
-408,10
+397,4
@@
public class AlignViewport extends AlignmentViewport
// TODO implement for applet
}
// TODO implement for applet
}
- @Override
- public boolean isNormaliseHMMSequenceLogo()
- {
- return normaliseHMMSequenceLogo;
- }
-
}
}