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position of bioinformatics
[jalview.git]
/
src
/
jalview
/
gui
/
AnnotationPanel.java
diff --git
a/src/jalview/gui/AnnotationPanel.java
b/src/jalview/gui/AnnotationPanel.java
index
f14b199
..
77f557b
100755
(executable)
--- a/
src/jalview/gui/AnnotationPanel.java
+++ b/
src/jalview/gui/AnnotationPanel.java
@@
-31,6
+31,8
@@
public class AnnotationPanel extends JPanel implements MouseListener, MouseMotio
\r
boolean fastPaint = false;
\r
\r
\r
boolean fastPaint = false;
\r
\r
+ public static int GRAPH_HEIGHT = 40;
\r
+
\r
\r
\r
public AnnotationPanel(AlignmentPanel ap)
\r
\r
\r
public AnnotationPanel(AlignmentPanel ap)
\r
@@
-70,7
+72,7
@@
public class AnnotationPanel extends JPanel implements MouseListener, MouseMotio
aa[i].height += 16;
\r
\r
if (aa[i].isGraph)
\r
aa[i].height += 16;
\r
\r
if (aa[i].isGraph)
\r
- aa[i].height += 50;
\r
+ aa[i].height += GRAPH_HEIGHT;
\r
\r
if(aa[i].height==0)
\r
aa[i].height = 20;
\r
\r
if(aa[i].height==0)
\r
aa[i].height = 20;
\r
@@
-310,7
+312,14
@@
public class AnnotationPanel extends JPanel implements MouseListener, MouseMotio
\r
int res = evt.getX() / av.getCharWidth() + av.getStartRes();
\r
if(row>-1 && res<aa[row].annotations.length && aa[row].annotations[res]!=null)
\r
\r
int res = evt.getX() / av.getCharWidth() + av.getStartRes();
\r
if(row>-1 && res<aa[row].annotations.length && aa[row].annotations[res]!=null)
\r
+ {
\r
this.setToolTipText(aa[row].annotations[res].description);
\r
this.setToolTipText(aa[row].annotations[res].description);
\r
+ StringBuffer text = new StringBuffer("Sequence position " + (res + 1) +
\r
+ " " +
\r
+ aa[row].annotations[res].description);
\r
+ ap.alignFrame.statusBar.setText(text.toString());
\r
+ }
\r
+
\r
\r
}
\r
public void mouseClicked(MouseEvent evt) {}
\r
\r
}
\r
public void mouseClicked(MouseEvent evt) {}
\r
@@
-334,21
+343,23
@@
public class AnnotationPanel extends JPanel implements MouseListener, MouseMotio
ap.annotationPanel.getHeight(),
\r
BufferedImage.TYPE_INT_RGB);
\r
gg = (Graphics2D) image.getGraphics();
\r
ap.annotationPanel.getHeight(),
\r
BufferedImage.TYPE_INT_RGB);
\r
gg = (Graphics2D) image.getGraphics();
\r
- gg.setColor(Color.white);
\r
- gg.fillRect(0, 0, imgWidth, getHeight());
\r
gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
\r
RenderingHints.VALUE_ANTIALIAS_ON);
\r
gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
\r
RenderingHints.VALUE_ANTIALIAS_ON);
\r
- fm = gg.getFontMetrics();
\r
- gg.setFont(av.getFont());
\r
\r
\r
+ gg.setFont(av.getFont());
\r
+ fm = gg.getFontMetrics();
\r
\r
drawComponent( gg, av.startRes, av.endRes+1);
\r
g.drawImage( image, 0, 0, this);
\r
\r
drawComponent( gg, av.startRes, av.endRes+1);
\r
g.drawImage( image, 0, 0, this);
\r
+
\r
}
\r
\r
public void fastPaint(int horizontal)
\r
{
\r
}
\r
\r
public void fastPaint(int horizontal)
\r
{
\r
- if(image==null || horizontal ==0)
\r
+ if( horizontal == 0
\r
+ || av.alignment.getAlignmentAnnotation()==null
\r
+ || av.alignment.getAlignmentAnnotation().length<1
\r
+ )
\r
{
\r
repaint();
\r
return;
\r
{
\r
repaint();
\r
return;
\r
@@
-385,6
+396,8
@@
public class AnnotationPanel extends JPanel implements MouseListener, MouseMotio
g.fillRect(0,0,(endRes-startRes) *av.charWidth, getHeight());
\r
if(av.alignment.getAlignmentAnnotation()==null || av.alignment.getAlignmentAnnotation().length<1)
\r
{
\r
g.fillRect(0,0,(endRes-startRes) *av.charWidth, getHeight());
\r
if(av.alignment.getAlignmentAnnotation()==null || av.alignment.getAlignmentAnnotation().length<1)
\r
{
\r
+ g.setColor(Color.white);
\r
+ g.fillRect(0,0,getWidth(), getHeight());
\r
g.setColor(Color.black);
\r
g.drawString("Alignment has no annotations",20,15);
\r
return;
\r
g.setColor(Color.black);
\r
g.drawString("Alignment has no annotations",20,15);
\r
return;
\r
@@
-398,6
+411,7
@@
public class AnnotationPanel extends JPanel implements MouseListener, MouseMotio
int iconOffset = av.charHeight/2;
\r
boolean validRes = false;
\r
//\u03B2 \u03B1
\r
int iconOffset = av.charHeight/2;
\r
boolean validRes = false;
\r
//\u03B2 \u03B1
\r
+
\r
for(int i=0; i<aa.length; i++)
\r
{
\r
AlignmentAnnotation row = aa[i];
\r
for(int i=0; i<aa.length; i++)
\r
{
\r
AlignmentAnnotation row = aa[i];
\r
@@
-441,9
+455,7
@@
public class AnnotationPanel extends JPanel implements MouseListener, MouseMotio
\r
if(validRes && row.annotations[j].displayCharacter.length()>0)
\r
{
\r
\r
if(validRes && row.annotations[j].displayCharacter.length()>0)
\r
{
\r
- int charOffset = (av.charWidth -
\r
- fm.charWidth(row.annotations[j].displayCharacter.
\r
- charAt(0))) / 2;
\r
+ int charOffset = (av.charWidth - fm.charWidth(row.annotations[j].displayCharacter.charAt(0)))/2;
\r
g.setColor( row.annotations[j].colour);
\r
if(j==0)
\r
{
\r
g.setColor( row.annotations[j].colour);
\r
if(j==0)
\r
{
\r
@@
-497,7
+509,7
@@
public class AnnotationPanel extends JPanel implements MouseListener, MouseMotio
if (validRes && row.isGraph)
\r
{
\r
g.setColor(new Color(0,0,180));
\r
if (validRes && row.isGraph)
\r
{
\r
g.setColor(new Color(0,0,180));
\r
- int height = (int)((row.annotations[j].value / row.graphMax)*50);
\r
+ int height = (int)((row.annotations[j].value / row.graphMax)*GRAPH_HEIGHT);
\r
\r
if(row.windowLength>1)
\r
{
\r
\r
if(row.windowLength>1)
\r
{
\r
@@
-511,10
+523,10
@@
public class AnnotationPanel extends JPanel implements MouseListener, MouseMotio
}
\r
\r
total/=row.windowLength;
\r
}
\r
\r
total/=row.windowLength;
\r
- height = (int)( (total / row.graphMax) *50);
\r
+ height = (int)( (total / row.graphMax) *GRAPH_HEIGHT);
\r
\r
}
\r
\r
}
\r
-
\r
+ g.setColor(row.annotations[j].colour);
\r
g.fillRect(x, y-height, av.charWidth, height );
\r
}
\r
\r
g.fillRect(x, y-height, av.charWidth, height );
\r
}
\r
\r
@@
-565,7
+577,7
@@
public class AnnotationPanel extends JPanel implements MouseListener, MouseMotio
for(int j=0; j<aa.annotations.length; j++)
\r
{
\r
g.setColor(new Color(0, 0, 180));
\r
for(int j=0; j<aa.annotations.length; j++)
\r
{
\r
g.setColor(new Color(0, 0, 180));
\r
- int height = (int) ( (aa.annotations[j].value / aa.graphMax) * 50);
\r
+ int height = (int) ( (aa.annotations[j].value / aa.graphMax) * GRAPH_HEIGHT );
\r
g.fillRect(x, y - height, av.charWidth, height);
\r
x+=av.charWidth;
\r
}
\r
g.fillRect(x, y - height, av.charWidth, height);
\r
x+=av.charWidth;
\r
}
\r