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added description of alignment quality scores and separated
[jalview.git]
/
src
/
jalview
/
gui
/
OverviewPanel.java
diff --git
a/src/jalview/gui/OverviewPanel.java
b/src/jalview/gui/OverviewPanel.java
index
c690490
..
7ffac1e
100755
(executable)
--- a/
src/jalview/gui/OverviewPanel.java
+++ b/
src/jalview/gui/OverviewPanel.java
@@
-65,7
+65,9
@@
public class OverviewPanel extends JPanel implements Runnable
\r
sr = new SequenceRenderer(av);
\r
sr.renderGaps( false );
\r
\r
sr = new SequenceRenderer(av);
\r
sr.renderGaps( false );
\r
+ sr.forOverview = true;
\r
fr = new FeatureRenderer(av);
\r
fr = new FeatureRenderer(av);
\r
+ fr.overview = true;
\r
\r
\r
// scale the initial size of overviewpanel to shape of alignment
\r
\r
\r
// scale the initial size of overviewpanel to shape of alignment
\r
@@
-245,11
+247,10
@@
public class OverviewPanel extends JPanel implements Runnable
\r
if (av.showSequenceFeatures)
\r
{
\r
\r
if (av.showSequenceFeatures)
\r
{
\r
- fr.featuresDisplayed = ap.seqPanel.seqCanvas.getFeatureRenderer().
\r
- featuresDisplayed;
\r
fr.featureGroups = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups;
\r
fr.featureColours = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours;
\r
fr.transparency = ap.seqPanel.seqCanvas.getFeatureRenderer().transparency;
\r
fr.featureGroups = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups;
\r
fr.featureColours = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours;
\r
fr.transparency = ap.seqPanel.seqCanvas.getFeatureRenderer().transparency;
\r
+ fr.sequenceFeatures = ap.seqPanel.seqCanvas.getFeatureRenderer().sequenceFeatures;
\r
}
\r
\r
int alwidth = av.alignment.getWidth();
\r
}
\r
\r
int alwidth = av.alignment.getWidth();
\r
@@
-275,14
+276,15
@@
public class OverviewPanel extends JPanel implements Runnable
float sampleRow = (float) alheight / (float) sequencesHeight;
\r
\r
int lastcol=-1, lastrow=-1;
\r
float sampleRow = (float) alheight / (float) sequencesHeight;
\r
\r
int lastcol=-1, lastrow=-1;
\r
- Color color = Color.white;
\r
- for (int col = 0; col < width; col++)
\r
+ int color = Color.white.getRGB();
\r
+ int row, col;
\r
+ for (row = 0; row < sequencesHeight; row++)
\r
{
\r
{
\r
- for (int row = 0; row < sequencesHeight; row++)
\r
- {
\r
+ for (col = 0; col < width; col++)
\r
+ {
\r
if((int)(col*sampleCol) == lastcol && (int)(row*sampleRow)==lastrow)
\r
{
\r
if((int)(col*sampleCol) == lastcol && (int)(row*sampleRow)==lastrow)
\r
{
\r
- miniMe.setRGB(col,row,color.getRGB());
\r
+ miniMe.setRGB(col,row,color);
\r
continue;
\r
}
\r
\r
continue;
\r
}
\r
\r
@@
-292,17
+294,28
@@
public class OverviewPanel extends JPanel implements Runnable
if(av.alignment.getSequenceAt(lastrow).getLength()>lastcol)
\r
{
\r
color = sr.getResidueBoxColour(
\r
if(av.alignment.getSequenceAt(lastrow).getLength()>lastcol)
\r
{
\r
color = sr.getResidueBoxColour(
\r
- av.alignment.getSequenceAt(lastrow), lastcol);
\r
+ av.alignment.getSequenceAt(lastrow), lastcol).getRGB();
\r
\r
if(av.showSequenceFeatures)
\r
\r
if(av.showSequenceFeatures)
\r
- color = fr.findFeatureColour(color, av.alignment.getSequenceAt(lastrow),
\r
- lastcol);
\r
+ color = fr.findFeatureColour(color, lastrow, lastcol);
\r
+
\r
+ }
\r
+ else
\r
+ {
\r
+ color = -1; //White
\r
+ }
\r
+
\r
+ miniMe.setRGB(col,row,color);
\r
\r
\r
- }
\r
\r
\r
- miniMe.setRGB(col,row,color.getRGB());
\r
+ }
\r
+ }
\r
\r
\r
- if (av.conservation != null)
\r
+ if (av.conservation != null)
\r
+ {
\r
+ for (col = 0; col < width; col++)
\r
+ {
\r
+ lastcol = (int) (col * sampleCol);
\r
{
\r
mg.translate(col, sequencesHeight);
\r
ap.annotationPanel.drawGraph(mg, av.conservation,
\r
{
\r
mg.translate(col, sequencesHeight);
\r
ap.annotationPanel.drawGraph(mg, av.conservation,
\r
@@
-310,11
+323,10
@@
public class OverviewPanel extends JPanel implements Runnable
graphHeight,
\r
(int) (col * sampleCol),
\r
(int) (col * sampleCol) + 1);
\r
graphHeight,
\r
(int) (col * sampleCol),
\r
(int) (col * sampleCol) + 1);
\r
- mg.translate(-col, -sequencesHeight);
\r
+ mg.translate( -col, -sequencesHeight);
\r
}
\r
}
\r
}
\r
}
\r
}
\r
}
\r
-
\r
System.gc();
\r
\r
resizing = false;
\r
System.gc();
\r
\r
resizing = false;
\r