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Merge remote-tracking branch 'origin/Tcoffee_JAL-1065' into develop
[jalview.git]
/
src
/
jalview
/
gui
/
SequenceRenderer.java
diff --git
a/src/jalview/gui/SequenceRenderer.java
b/src/jalview/gui/SequenceRenderer.java
index
e94fba4
..
b294282
100755
(executable)
--- a/
src/jalview/gui/SequenceRenderer.java
+++ b/
src/jalview/gui/SequenceRenderer.java
@@
-17,10
+17,14
@@
*/
package jalview.gui;
*/
package jalview.gui;
-import java.awt.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ColourSchemeI;
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import java.awt.Color;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
/**
* DOCUMENT ME!
/**
* DOCUMENT ME!
@@
-80,7
+84,7
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
public Color getResidueBoxColour(SequenceI seq, int i)
{
public Color getResidueBoxColour(SequenceI seq, int i)
{
- allGroups = av.alignment.findAllGroups(seq);
+ allGroups = av.getAlignment().findAllGroups(seq);
if (inCurrentSequenceGroup(i))
{
if (inCurrentSequenceGroup(i))
{
@@
-91,7
+95,7
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
}
else if (av.getShowBoxes())
{
}
else if (av.getShowBoxes())
{
- getBoxColour(av.globalColourScheme, seq, i);
+ getBoxColour(av.getGlobalColourScheme(), seq, i);
}
return resBoxColour;
}
return resBoxColour;
@@
-111,7
+115,7
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
{
if (cs != null)
{
{
if (cs != null)
{
- resBoxColour = cs.findColour(seq.getCharAt(i), i);
+ resBoxColour = cs.findColour(seq.getCharAt(i), i, seq);
}
else if (forOverview
&& !jalview.util.Comparison.isGap(seq.getCharAt(i)))
}
else if (forOverview
&& !jalview.util.Comparison.isGap(seq.getCharAt(i)))
@@
-205,7
+209,7
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
}
else if (av.getShowBoxes())
{
}
else if (av.getShowBoxes())
{
- getBoxColour(av.globalColourScheme, seq, i);
+ getBoxColour(av.getGlobalColourScheme(), seq, i);
}
}
}
}
@@
-328,7
+332,7
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
if (currentSequenceGroup.getShowNonconserved()) // todo optimize
{
// todo - use sequence group consensus
if (currentSequenceGroup.getShowNonconserved()) // todo optimize
{
// todo - use sequence group consensus
- s = getDisplayChar(av.consensus, i, s, '.');
+ s = getDisplayChar(av.getAlignmentConsensusAnnotation(), i, s, '.');
}
}
@@
-343,7
+347,7
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
if (av.getColourText())
{
getboxColour = true;
if (av.getColourText())
{
getboxColour = true;
- getBoxColour(av.globalColourScheme, seq, i);
+ getBoxColour(av.getGlobalColourScheme(), seq, i);
if (av.getShowBoxes())
{
if (av.getShowBoxes())
{
@@
-359,7
+363,7
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
{
if (!getboxColour)
{
{
if (!getboxColour)
{
- getBoxColour(av.globalColourScheme, seq, i);
+ getBoxColour(av.getGlobalColourScheme(), seq, i);
}
if (resBoxColour.getRed() + resBoxColour.getBlue()
}
if (resBoxColour.getRed() + resBoxColour.getBlue()
@@
-368,9
+372,9
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
graphics.setColor(av.textColour2);
}
}
graphics.setColor(av.textColour2);
}
}
- if (av.showUnconserved)
+ if (av.getShowUnconserved())
{
{
- s = getDisplayChar(av.consensus, i, s, '.');
+ s = getDisplayChar(av.getAlignmentConsensusAnnotation(), i, s, '.');
}
}