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command line hook for questionnaire url argument.
[jalview.git]
/
src
/
jalview
/
gui
/
SeqCanvas.java
diff --git
a/src/jalview/gui/SeqCanvas.java
b/src/jalview/gui/SeqCanvas.java
index
56e70ac
..
45bcf66
100755
(executable)
--- a/
src/jalview/gui/SeqCanvas.java
+++ b/
src/jalview/gui/SeqCanvas.java
@@
-418,7
+418,16
@@
public class SeqCanvas extends JComponent
String getMask()
\r
{
\r
String mask = "00";
\r
String getMask()
\r
{
\r
String mask = "00";
\r
- for (int i = av.alignment.getWidth(); i > 0; i /= 10)
\r
+ int maxWidth = 0;
\r
+ int tmp;
\r
+ for(int i=0; i<av.alignment.getHeight(); i++)
\r
+ {
\r
+ tmp = av.alignment.getSequenceAt(i).getEnd();
\r
+ if(tmp>maxWidth)
\r
+ maxWidth = tmp;
\r
+ }
\r
+
\r
+ for (int i = maxWidth; i > 0; i /= 10)
\r
{
\r
mask += "0";
\r
}
\r
{
\r
mask += "0";
\r
}
\r
@@
-466,7
+475,7
@@
public class SeqCanvas extends JComponent
\r
int endx;
\r
int ypos = hgap;
\r
\r
int endx;
\r
int ypos = hgap;
\r
- int maxwidth = av.alignment.getWidth();
\r
+ int maxwidth = av.alignment.getWidth()-1;
\r
\r
if(av.hasHiddenColumns)
\r
maxwidth = av.getColumnSelection().findColumnPosition(maxwidth)-1;
\r
\r
if(av.hasHiddenColumns)
\r
maxwidth = av.getColumnSelection().findColumnPosition(maxwidth)-1;
\r
@@
-554,14
+563,12
@@
public class SeqCanvas extends JComponent
annotations = new AnnotationPanel(av);
\r
\r
annotations.drawComponent( (Graphics2D) g, startRes, endx+1);
\r
annotations = new AnnotationPanel(av);
\r
\r
annotations.drawComponent( (Graphics2D) g, startRes, endx+1);
\r
- g.translate(0, -cHeight - ypos);
\r
+ g.translate(0, -cHeight - ypos -3);
\r
}
\r
g.setClip(clip);
\r
g.translate(-LABEL_WEST, 0);
\r
\r
ypos += cHeight+getAnnotationHeight()+hgap;
\r
}
\r
g.setClip(clip);
\r
g.translate(-LABEL_WEST, 0);
\r
\r
ypos += cHeight+getAnnotationHeight()+hgap;
\r
- if(av.showAnnotation)
\r
- ypos -= 3;
\r
\r
startRes += cWidth;
\r
}
\r
\r
startRes += cWidth;
\r
}
\r
@@
-756,11
+763,11
@@
public class SeqCanvas extends JComponent
}
\r
\r
if ( (sx <= (endRes-startRes)*av.charWidth) &&
\r
}
\r
\r
if ( (sx <= (endRes-startRes)*av.charWidth) &&
\r
- group.getSequences(false).
\r
+ group.getSequences(null).
\r
contains(av.alignment.getSequenceAt(i)))
\r
{
\r
if ((bottom == -1) &&
\r
contains(av.alignment.getSequenceAt(i)))
\r
{
\r
if ((bottom == -1) &&
\r
- !group.getSequences(false).contains(
\r
+ !group.getSequences(null).contains(
\r
av.alignment.getSequenceAt(i + 1)))
\r
{
\r
bottom = sy + av.charHeight;
\r
av.alignment.getSequenceAt(i + 1)))
\r
{
\r
bottom = sy + av.charHeight;
\r
@@
-769,7
+776,7
@@
public class SeqCanvas extends JComponent
if (!inGroup)
\r
{
\r
if (((top == -1) && (i == 0)) ||
\r
if (!inGroup)
\r
{
\r
if (((top == -1) && (i == 0)) ||
\r
- !group.getSequences(false).contains(
\r
+ !group.getSequences(null).contains(
\r
av.alignment.getSequenceAt(i - 1)))
\r
{
\r
top = sy;
\r
av.alignment.getSequenceAt(i - 1)))
\r
{
\r
top = sy;
\r