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JAL-969 - refactor initialisation of automatic annotation rows to base class
[jalview.git]
/
src
/
jalview
/
gui
/
SeqCanvas.java
diff --git
a/src/jalview/gui/SeqCanvas.java
b/src/jalview/gui/SeqCanvas.java
index
9e3f8a2
..
f982ccc
100755
(executable)
--- a/
src/jalview/gui/SeqCanvas.java
+++ b/
src/jalview/gui/SeqCanvas.java
@@
-105,7
+105,7
@@
public class SeqCanvas extends JComponent
for (int i = scalestartx; i < endx; i += 10)
{
int value = i;
for (int i = scalestartx; i < endx; i += 10)
{
int value = i;
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
value = av.getColumnSelection().adjustForHiddenColumns(value);
}
{
value = av.getColumnSelection().adjustForHiddenColumns(value);
}
@@
-137,22
+137,22
@@
public class SeqCanvas extends JComponent
FontMetrics fm = getFontMetrics(av.getFont());
ypos += av.charHeight;
FontMetrics fm = getFontMetrics(av.getFont());
ypos += av.charHeight;
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
startx = av.getColumnSelection().adjustForHiddenColumns(startx);
endx = av.getColumnSelection().adjustForHiddenColumns(endx);
}
{
startx = av.getColumnSelection().adjustForHiddenColumns(startx);
endx = av.getColumnSelection().adjustForHiddenColumns(endx);
}
- int maxwidth = av.alignment.getWidth();
- if (av.hasHiddenColumns)
+ int maxwidth = av.getAlignment().getWidth();
+ if (av.hasHiddenColumns())
{
maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
}
// WEST SCALE
{
maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
}
// WEST SCALE
- for (int i = 0; i < av.alignment.getHeight(); i++)
+ for (int i = 0; i < av.getAlignment().getHeight(); i++)
{
{
- SequenceI seq = av.alignment.getSequenceAt(i);
+ SequenceI seq = av.getAlignment().getSequenceAt(i);
int index = startx;
int value = -1;
int index = startx;
int value = -1;
@@
-165,7
+165,7
@@
public class SeqCanvas extends JComponent
continue;
}
continue;
}
- value = av.alignment.getSequenceAt(i).findPosition(index);
+ value = av.getAlignment().getSequenceAt(i).findPosition(index);
break;
}
break;
}
@@
-196,16
+196,16
@@
public class SeqCanvas extends JComponent
{
ypos += av.charHeight;
{
ypos += av.charHeight;
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
endx = av.getColumnSelection().adjustForHiddenColumns(endx);
}
SequenceI seq;
// EAST SCALE
{
endx = av.getColumnSelection().adjustForHiddenColumns(endx);
}
SequenceI seq;
// EAST SCALE
- for (int i = 0; i < av.alignment.getHeight(); i++)
+ for (int i = 0; i < av.getAlignment().getHeight(); i++)
{
{
- seq = av.alignment.getSequenceAt(i);
+ seq = av.getAlignment().getSequenceAt(i);
int index = endx;
int value = -1;
int index = endx;
int value = -1;
@@
-425,9
+425,9
@@
public class SeqCanvas extends JComponent
String mask = "00";
int maxWidth = 0;
int tmp;
String mask = "00";
int maxWidth = 0;
int tmp;
- for (int i = 0; i < av.alignment.getHeight(); i++)
+ for (int i = 0; i < av.getAlignment().getHeight(); i++)
{
{
- tmp = av.alignment.getSequenceAt(i).getEnd();
+ tmp = av.getAlignment().getSequenceAt(i).getEnd();
if (tmp > maxWidth)
{
maxWidth = tmp;
if (tmp > maxWidth)
{
maxWidth = tmp;
@@
-485,9
+485,9
@@
public class SeqCanvas extends JComponent
int endx;
int ypos = hgap;
int endx;
int ypos = hgap;
- int maxwidth = av.alignment.getWidth() - 1;
+ int maxwidth = av.getAlignment().getWidth() - 1;
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
}
{
maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
}
@@
-523,7
+523,7
@@
public class SeqCanvas extends JComponent
drawNorthScale(g, startRes, endx, ypos);
}
drawNorthScale(g, startRes, endx, ypos);
}
- if (av.hasHiddenColumns && av.showHiddenMarkers)
+ if (av.hasHiddenColumns() && av.showHiddenMarkers)
{
g.setColor(Color.blue);
int res;
{
g.setColor(Color.blue);
int res;
@@
-620,7
+620,7
@@
public class SeqCanvas extends JComponent
void drawPanel(Graphics g1, int startRes, int endRes, int startSeq,
int endSeq, int offset)
{
void drawPanel(Graphics g1, int startRes, int endRes, int startSeq,
int endSeq, int offset)
{
- if (!av.hasHiddenColumns)
+ if (!av.hasHiddenColumns())
{
draw(g1, startRes, endRes, startSeq, endSeq, offset);
}
{
draw(g1, startRes, endRes, startSeq, endSeq, offset);
}
@@
-690,14
+690,14
@@
public class SeqCanvas extends JComponent
// ///////////////////////////
for (int i = startSeq; i < endSeq; i++)
{
// ///////////////////////////
for (int i = startSeq; i < endSeq; i++)
{
- nextSeq = av.alignment.getSequenceAt(i);
+ nextSeq = av.getAlignment().getSequenceAt(i);
if (nextSeq == null)
{
// occasionally, a race condition occurs such that the alignment row is
// empty
continue;
}
if (nextSeq == null)
{
// occasionally, a race condition occurs such that the alignment row is
// empty
continue;
}
- sr.drawSequence(nextSeq, av.alignment.findAllGroups(nextSeq),
+ sr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq),
startRes, endRes, offset + ((i - startSeq) * av.charHeight));
if (av.showSequenceFeatures)
startRes, endRes, offset + ((i - startSeq) * av.charHeight));
if (av.showSequenceFeatures)
@@
-734,7
+734,7
@@
public class SeqCanvas extends JComponent
}
if (av.getSelectionGroup() != null
}
if (av.getSelectionGroup() != null
- || av.alignment.getGroups().size() > 0)
+ || av.getAlignment().getGroups().size() > 0)
{
drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset);
}
{
drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset);
}
@@
-757,9
+757,9
@@
public class SeqCanvas extends JComponent
int groupIndex = -1;
int visWidth = (endRes - startRes + 1) * av.charWidth;
int groupIndex = -1;
int visWidth = (endRes - startRes + 1) * av.charWidth;
- if ((group == null) && (av.alignment.getGroups().size() > 0))
+ if ((group == null) && (av.getAlignment().getGroups().size() > 0))
{
{
- group = (SequenceGroup) av.alignment.getGroups().elementAt(0);
+ group = (SequenceGroup) av.getAlignment().getGroups().elementAt(0);
groupIndex = 0;
}
groupIndex = 0;
}
@@
-786,11
+786,11
@@
public class SeqCanvas extends JComponent
if ((sx <= (endRes - startRes) * av.charWidth)
&& group.getSequences(null).contains(
if ((sx <= (endRes - startRes) * av.charWidth)
&& group.getSequences(null).contains(
- av.alignment.getSequenceAt(i)))
+ av.getAlignment().getSequenceAt(i)))
{
if ((bottom == -1)
&& !group.getSequences(null).contains(
{
if ((bottom == -1)
&& !group.getSequences(null).contains(
- av.alignment.getSequenceAt(i + 1)))
+ av.getAlignment().getSequenceAt(i + 1)))
{
bottom = sy + av.charHeight;
}
{
bottom = sy + av.charHeight;
}
@@
-799,7
+799,7
@@
public class SeqCanvas extends JComponent
{
if (((top == -1) && (i == 0))
|| !group.getSequences(null).contains(
{
if (((top == -1) && (i == 0))
|| !group.getSequences(null).contains(
- av.alignment.getSequenceAt(i - 1)))
+ av.getAlignment().getSequenceAt(i - 1)))
{
top = sy;
}
{
top = sy;
}
@@
-915,15
+915,15
@@
public class SeqCanvas extends JComponent
g.setStroke(new BasicStroke());
g.setStroke(new BasicStroke());
- if (groupIndex >= av.alignment.getGroups().size())
+ if (groupIndex >= av.getAlignment().getGroups().size())
{
break;
}
{
break;
}
- group = (SequenceGroup) av.alignment.getGroups().elementAt(
+ group = (SequenceGroup) av.getAlignment().getGroups().elementAt(
groupIndex);
groupIndex);
- } while (groupIndex < av.alignment.getGroups().size());
+ } while (groupIndex < av.getAlignment().getGroups().size());
}
}