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JAL-2600 Abandoned fastpaint for resize; now full repaint, single call
[jalview.git]
/
src
/
jalview
/
gui
/
SequenceRenderer.java
diff --git
a/src/jalview/gui/SequenceRenderer.java
b/src/jalview/gui/SequenceRenderer.java
index
311439a
..
36825ea
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.api.AlignViewportI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
-import jalview.schemes.CollectionColourSchemeI;
+import jalview.renderer.ResidueShaderI;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
import jalview.util.Comparison;
import java.awt.Color;
import jalview.util.Comparison;
import java.awt.Color;
@@
-34,7
+35,7
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
{
final static int CHAR_TO_UPPER = 'A' - 'a';
{
final static int CHAR_TO_UPPER = 'A' - 'a';
- AlignViewport av;
+ AlignViewportI av;
FontMetrics fm;
FontMetrics fm;
@@
-53,14
+54,13
@@
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(AlignViewportI viewport)
{
{
- this.av = av;
+ this.av = viewport;
}
/**
}
/**
@@
-83,8
+83,7
@@
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);
@@
-98,7
+97,7
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
}
else if (av.getShowBoxes())
{
}
else if (av.getShowBoxes())
{
- getBoxColour(av.getViewportColourScheme(), seq, i);
+ getBoxColour(av.getResidueShading(), seq, i);
}
return resBoxColour;
}
return resBoxColour;
@@
-111,20
+110,18
@@
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;
}
@@
-132,19
+129,18
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
/**
* DOCUMENT ME!
*
/**
* DOCUMENT ME!
*
- * @param collectionColourSchemeI
+ * @param shader
* DOCUMENT ME!
* @param seq
* DOCUMENT ME!
* @param i
* DOCUMENT ME!
*/
* DOCUMENT ME!
* @param seq
* DOCUMENT ME!
* @param i
* DOCUMENT ME!
*/
- void getBoxColour(CollectionColourSchemeI collectionColourSchemeI,
- SequenceI seq, int i)
+ void getBoxColour(ResidueShaderI shader, SequenceI seq, int i)
{
{
- if (collectionColourSchemeI != null)
+ if (shader.getColourScheme() != null)
{
{
- resBoxColour = collectionColourSchemeI.findColour(seq.getCharAt(i),
+ resBoxColour = shader.findColour(seq.getCharAt(i),
i, seq);
}
else if (forOverview && !Comparison.isGap(seq.getCharAt(i)))
i, seq);
}
else if (forOverview && !Comparison.isGap(seq.getCharAt(i)))
@@
-186,7
+182,7
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
drawBoxes(seq, start, end, y1);
drawBoxes(seq, start, end, y1);
- if (av.validCharWidth)
+ if (av.isValidCharWidth())
{
drawText(seq, start, end, y1);
}
{
drawText(seq, start, end, y1);
}
@@
-242,7
+238,7
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
}
else if (av.getShowBoxes())
{
}
else if (av.getShowBoxes())
{
- getBoxColour(av.getViewportColourScheme(), seq, i);
+ getBoxColour(av.getResidueShading(), seq, i);
}
}
}
}
@@
-388,7
+384,7
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
if (av.getColourText())
{
getboxColour = true;
if (av.getColourText())
{
getboxColour = true;
- getBoxColour(av.getViewportColourScheme(), seq, i);
+ getBoxColour(av.getResidueShading(), seq, i);
if (av.getShowBoxes())
{
if (av.getShowBoxes())
{
@@
-404,7
+400,7
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
{
if (!getboxColour)
{
{
if (!getboxColour)
{
- getBoxColour(av.getViewportColourScheme(), seq, i);
+ getBoxColour(av.getResidueShading(), seq, i);
}
if (resBoxColour.getRed() + resBoxColour.getBlue()
}
if (resBoxColour.getRed() + resBoxColour.getBlue()