git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
added description of alignment quality scores and separated
[jalview.git]
/
src
/
jalview
/
gui
/
SequenceRenderer.java
diff --git
a/src/jalview/gui/SequenceRenderer.java
b/src/jalview/gui/SequenceRenderer.java
index
0c41152
..
0e4312a
100755
(executable)
--- a/
src/jalview/gui/SequenceRenderer.java
+++ b/
src/jalview/gui/SequenceRenderer.java
@@
-40,6
+40,7
@@
public class SequenceRenderer
Color resBoxColour;
\r
Graphics graphics;
\r
boolean monospacedFont;
\r
Color resBoxColour;
\r
Graphics graphics;
\r
boolean monospacedFont;
\r
+ boolean forOverview = false;
\r
\r
/**
\r
* Creates a new SequenceRenderer object.
\r
\r
/**
\r
* Creates a new SequenceRenderer object.
\r
@@
-95,9
+96,13
@@
public class SequenceRenderer
{
\r
resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i);
\r
}
\r
{
\r
resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i);
\r
}
\r
+ else if(forOverview && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
\r
+ {
\r
+ resBoxColour = Color.lightGray;
\r
+ }
\r
else
\r
{
\r
else
\r
{
\r
- resBoxColour = Color.white;
\r
+ resBoxColour = Color.white;
\r
}
\r
}
\r
\r
}
\r
}
\r
\r
@@
-115,19
+120,19
@@
public class SequenceRenderer
* @param height DOCUMENT ME!
\r
*/
\r
public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,
\r
* @param height DOCUMENT ME!
\r
*/
\r
public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,
\r
- int start, int end, int x1, int y1, int width, int height)
\r
+ int start, int end, int y1)
\r
{
\r
allGroups = sg;
\r
\r
graphics = g;
\r
\r
{
\r
allGroups = sg;
\r
\r
graphics = g;
\r
\r
- drawBoxes(seq, start, end, x1, y1, (int) width, height);
\r
+ drawBoxes(seq, start, end, y1);
\r
\r
fm = g.getFontMetrics();
\r
\r
monospacedFont = fm.getStringBounds("M",g).getWidth()==fm.getStringBounds("|",g).getWidth();
\r
\r
\r
fm = g.getFontMetrics();
\r
\r
monospacedFont = fm.getStringBounds("M",g).getWidth()==fm.getStringBounds("|",g).getWidth();
\r
\r
- drawText(seq, start, end, x1, y1, (int) width, height);
\r
+ drawText(seq, start, end, y1);
\r
}
\r
\r
/**
\r
}
\r
\r
/**
\r
@@
-141,14
+146,13
@@
public class SequenceRenderer
* @param width DOCUMENT ME!
\r
* @param height DOCUMENT ME!
\r
*/
\r
* @param width DOCUMENT ME!
\r
* @param height DOCUMENT ME!
\r
*/
\r
- public synchronized void drawBoxes(SequenceI seq, int start, int end, int x1, int y1,
\r
- int width, int height)
\r
+ public synchronized void drawBoxes(SequenceI seq, int start, int end, int y1)
\r
{
\r
int i = start;
\r
int length = seq.getLength();
\r
\r
int curStart = -1;
\r
{
\r
int i = start;
\r
int length = seq.getLength();
\r
\r
int curStart = -1;
\r
- int curWidth = width;
\r
+ int curWidth = av.charWidth;
\r
\r
Color tempColour = null;
\r
\r
\r
Color tempColour = null;
\r
\r
@@
-176,26
+180,26
@@
public class SequenceRenderer
{
\r
if (tempColour != null)
\r
{
\r
{
\r
if (tempColour != null)
\r
{
\r
- graphics.fillRect(x1 + (width * (curStart - start)), y1,
\r
- curWidth, height);
\r
+ graphics.fillRect( av.charWidth * (curStart - start), y1,
\r
+ curWidth, av.charHeight);
\r
}
\r
\r
graphics.setColor(resBoxColour);
\r
\r
curStart = i;
\r
}
\r
\r
graphics.setColor(resBoxColour);
\r
\r
curStart = i;
\r
- curWidth = width;
\r
+ curWidth = av.charWidth;
\r
tempColour = resBoxColour;
\r
}
\r
else
\r
{
\r
tempColour = resBoxColour;
\r
}
\r
else
\r
{
\r
- curWidth += width;
\r
+ curWidth += av.charWidth;
\r
}
\r
\r
i++;
\r
}
\r
\r
}
\r
\r
i++;
\r
}
\r
\r
- graphics.fillRect(x1 + (width * (curStart - start)), y1, curWidth,
\r
- height);
\r
+ graphics.fillRect( av.charWidth * (curStart - start), y1, curWidth,
\r
+ av.charHeight);
\r
\r
}
\r
\r
\r
}
\r
\r
@@
-210,10
+214,9
@@
public class SequenceRenderer
* @param width DOCUMENT ME!
\r
* @param height DOCUMENT ME!
\r
*/
\r
* @param width DOCUMENT ME!
\r
* @param height DOCUMENT ME!
\r
*/
\r
- public void drawText(SequenceI seq, int start, int end, int x1, int y1,
\r
- int width, int height)
\r
+ public void drawText(SequenceI seq, int start, int end, int y1)
\r
{
\r
{
\r
- y1 += height - height / 5; // height/5 replaces pady
\r
+ y1 += av.charHeight - av.charHeight / 5; // height/5 replaces pady
\r
int charOffset = 0;
\r
char s;
\r
\r
int charOffset = 0;
\r
char s;
\r
\r
@@
-224,7
+227,7
@@
public class SequenceRenderer
\r
if(monospacedFont && av.showText && allGroups.length==0 && !av.getColourText())
\r
{
\r
\r
if(monospacedFont && av.showText && allGroups.length==0 && !av.getColourText())
\r
{
\r
- graphics.drawString(seq.getSequence(start, end + 1), x1, y1);
\r
+ graphics.drawString(seq.getSequence(start, end + 1), 0, y1);
\r
}
\r
else
\r
{
\r
}
\r
else
\r
{
\r
@@
-272,12
+275,15
@@
public class SequenceRenderer
}
\r
}
\r
\r
}
\r
}
\r
\r
- charOffset = (width - fm.charWidth(s)) / 2;
\r
+ charOffset = (av.charWidth - fm.charWidth(s)) / 2;
\r
+
\r
+ // System.out.print(s);
\r
graphics.drawString(String.valueOf(s),
\r
graphics.drawString(String.valueOf(s),
\r
- charOffset + x1 + width * (i - start),
\r
+ charOffset + av.charWidth * (i - start),
\r
y1);
\r
\r
}
\r
y1);
\r
\r
}
\r
+ // System.out.println("\n");
\r
}
\r
}
\r
\r
}
\r
}
\r
\r