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Merge branch 'develop' into bug/JAL-2255_seq-fetcher-broken-on-linux
[jalview.git]
/
src
/
jalview
/
gui
/
SequenceRenderer.java
diff --git
a/src/jalview/gui/SequenceRenderer.java
b/src/jalview/gui/SequenceRenderer.java
index
64fe053
..
1c0420d
100755
(executable)
--- a/
src/jalview/gui/SequenceRenderer.java
+++ b/
src/jalview/gui/SequenceRenderer.java
@@
-20,10
+20,11
@@
*/
package jalview.gui;
*/
package jalview.gui;
-import jalview.api.FeatureRenderer;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
-import jalview.schemes.ColourSchemeI;
+import jalview.renderer.ResidueShaderI;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
+import jalview.util.Comparison;
import java.awt.Color;
import java.awt.FontMetrics;
import java.awt.Color;
import java.awt.FontMetrics;
@@
-52,14
+53,13
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
boolean forOverview = false;
/**
boolean forOverview = false;
/**
- * Creates a new SequenceRenderer object.
+ * Creates a new SequenceRenderer object
*
*
- * @param av
- * DOCUMENT ME!
+ * @param viewport
*/
*/
- public SequenceRenderer(AlignViewport av)
+ public SequenceRenderer(AlignViewport viewport)
{
{
- this.av = av;
+ this.av = viewport;
}
/**
}
/**
@@
-82,8
+82,7
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
this.renderGaps = renderGaps;
}
this.renderGaps = renderGaps;
}
- @Override
- public Color getResidueBoxColour(SequenceI seq, int i)
+ protected Color getResidueBoxColour(SequenceI seq, int i)
{
// rate limiting step when rendering overview for lots of groups
allGroups = av.getAlignment().findAllGroups(seq);
{
// rate limiting step when rendering overview for lots of groups
allGroups = av.getAlignment().findAllGroups(seq);
@@
-92,12
+91,12
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
{
if (currentSequenceGroup.getDisplayBoxes())
{
{
if (currentSequenceGroup.getDisplayBoxes())
{
- getBoxColour(currentSequenceGroup.cs, seq, i);
+ getBoxColour(currentSequenceGroup.getGroupColourScheme(), seq, i);
}
}
else if (av.getShowBoxes())
{
}
}
else if (av.getShowBoxes())
{
- getBoxColour(av.getGlobalColourScheme(), seq, i);
+ getBoxColour(av.getResidueShading(), seq, i);
}
return resBoxColour;
}
return resBoxColour;
@@
-110,20
+109,18
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
*
* @param seq
* @param position
*
* @param seq
* @param position
- * @param fr
+ * @param finder
* @return
*/
@Override
public Color getResidueColour(final SequenceI seq, int position,
* @return
*/
@Override
public Color getResidueColour(final SequenceI seq, int position,
- FeatureRenderer fr)
+ FeatureColourFinder finder)
{
{
- // TODO replace 8 or so code duplications with calls to this method
- // (refactored as needed)
Color col = getResidueBoxColour(seq, position);
Color col = getResidueBoxColour(seq, position);
- if (fr != null)
+ if (finder != null)
{
{
- col = fr.findFeatureColour(col, seq, position);
+ col = finder.findFeatureColour(col, seq, position);
}
return col;
}
}
return col;
}
@@
-131,21
+128,21
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
/**
* DOCUMENT ME!
*
/**
* DOCUMENT ME!
*
- * @param cs
+ * @param shader
* DOCUMENT ME!
* @param seq
* DOCUMENT ME!
* @param i
* DOCUMENT ME!
*/
* DOCUMENT ME!
* @param seq
* DOCUMENT ME!
* @param i
* DOCUMENT ME!
*/
- void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
+ void getBoxColour(ResidueShaderI shader, SequenceI seq, int i)
{
{
- if (cs != null)
+ if (shader != null)
{
{
- resBoxColour = cs.findColour(seq.getCharAt(i), i, seq);
+ resBoxColour = shader.findColour(seq.getCharAt(i),
+ i, seq);
}
}
- else if (forOverview
- && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
+ else if (forOverview && !Comparison.isGap(seq.getCharAt(i)))
{
resBoxColour = Color.lightGray;
}
{
resBoxColour = Color.lightGray;
}
@@
-234,14
+231,14
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
{
if (currentSequenceGroup.getDisplayBoxes())
{
{
if (currentSequenceGroup.getDisplayBoxes())
{
- getBoxColour(currentSequenceGroup.cs, seq, i);
+ getBoxColour(currentSequenceGroup.getGroupColourScheme(), seq,
+ i);
}
}
else if (av.getShowBoxes())
{
}
}
else if (av.getShowBoxes())
{
- getBoxColour(av.getGlobalColourScheme(), seq, i);
+ getBoxColour(av.getResidueShading(), seq, i);
}
}
-
}
if (resBoxColour != tempColour)
}
if (resBoxColour != tempColour)
@@
-345,7
+342,8
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
|| currentSequenceGroup.getColourText())
{
getboxColour = true;
|| currentSequenceGroup.getColourText())
{
getboxColour = true;
- getBoxColour(currentSequenceGroup.cs, seq, i);
+ getBoxColour(currentSequenceGroup.getGroupColourScheme(), seq,
+ i);
if (currentSequenceGroup.getColourText())
{
if (currentSequenceGroup.getColourText())
{
@@
-385,7
+383,7
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
if (av.getColourText())
{
getboxColour = true;
if (av.getColourText())
{
getboxColour = true;
- getBoxColour(av.getGlobalColourScheme(), seq, i);
+ getBoxColour(av.getResidueShading(), seq, i);
if (av.getShowBoxes())
{
if (av.getShowBoxes())
{
@@
-401,7
+399,7
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
{
if (!getboxColour)
{
{
if (!getboxColour)
{
- getBoxColour(av.getGlobalColourScheme(), seq, i);
+ getBoxColour(av.getResidueShading(), seq, i);
}
if (resBoxColour.getRed() + resBoxColour.getBlue()
}
if (resBoxColour.getRed() + resBoxColour.getBlue()