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JAL-2388 Made ViewportRanges final
[jalview.git]
/
src
/
jalview
/
appletgui
/
AlignViewport.java
diff --git
a/src/jalview/appletgui/AlignViewport.java
b/src/jalview/appletgui/AlignViewport.java
index
b025f64
..
b289be7
100644
(file)
--- a/
src/jalview/appletgui/AlignViewport.java
+++ b/
src/jalview/appletgui/AlignViewport.java
@@
-32,9
+32,9
@@
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.renderer.ResidueShader;
import jalview.schemes.ColourSchemeProperty;
import jalview.schemes.UserColourScheme;
import jalview.schemes.ColourSchemeProperty;
import jalview.schemes.UserColourScheme;
-import jalview.structure.CommandListener;
import jalview.structure.SelectionSource;
import jalview.structure.StructureSelectionManager;
import jalview.structure.VamsasSource;
import jalview.structure.SelectionSource;
import jalview.structure.StructureSelectionManager;
import jalview.structure.VamsasSource;
@@
-43,7
+43,7
@@
import jalview.viewmodel.AlignmentViewport;
import java.awt.Font;
public class AlignViewport extends AlignmentViewport implements
import java.awt.Font;
public class AlignViewport extends AlignmentViewport implements
- SelectionSource, VamsasSource, CommandListener
+ SelectionSource
{
boolean cursorMode = false;
{
boolean cursorMode = false;
@@
-70,16
+70,13
@@
public class AlignViewport extends AlignmentViewport implements
public AlignViewport(AlignmentI al, JalviewLite applet)
{
public AlignViewport(AlignmentI al, JalviewLite applet)
{
- super();
+ super(al);
calculator = new jalview.workers.AlignCalcManager();
this.applet = applet;
calculator = new jalview.workers.AlignCalcManager();
this.applet = applet;
- alignment = al;
+
// we always pad gaps
this.setPadGaps(true);
// we always pad gaps
this.setPadGaps(true);
- this.startRes = 0;
- this.endRes = al.getWidth() - 1;
- this.startSeq = 0;
- this.endSeq = al.getHeight() - 1;
+
if (applet != null)
{
// get the width and height scaling factors if they were specified
if (applet != null)
{
// get the width and height scaling factors if they were specified
@@
-208,18
+205,19
@@
public class AlignViewport extends AlignmentViewport implements
if (colour != null)
{
if (colour != null)
{
- globalColourScheme = ColourSchemeProperty.getColourScheme(
- alignment, colour);
- if (globalColourScheme != null)
+ residueShading = new ResidueShader(
+ ColourSchemeProperty.getColourScheme(alignment, colour));
+ if (residueShading != null)
{
{
- globalColourScheme.setConsensus(hconsensus);
+ residueShading.setConsensus(hconsensus);
}
}
if (applet.getParameter("userDefinedColour") != null)
{
}
}
if (applet.getParameter("userDefinedColour") != null)
{
- ((UserColourScheme) globalColourScheme).parseAppletParameter(applet
- .getParameter("userDefinedColour"));
+ residueShading = new ResidueShader(
+ new UserColourScheme(
+ applet.getParameter("userDefinedColour")));
}
}
initAutoAnnotation();
}
}
initAutoAnnotation();
@@
-297,7
+295,7
@@
public class AlignViewport extends AlignmentViewport implements
public void resetSeqLimits(int height)
{
public void resetSeqLimits(int height)
{
- setEndSeq(height / getCharHeight());
+ ranges.setEndSeq(height / getCharHeight());
}
public void setCurrentTree(NJTree tree)
}
public void setCurrentTree(NJTree tree)