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JAL-516 JAL-759 JAL-1066 group & group colourscheme always gets notified when group...
[jalview.git]
/
src
/
jalview
/
appletgui
/
SeqCanvas.java
diff --git
a/src/jalview/appletgui/SeqCanvas.java
b/src/jalview/appletgui/SeqCanvas.java
index
26da08b
..
c7a8232
100755
(executable)
--- a/
src/jalview/appletgui/SeqCanvas.java
+++ b/
src/jalview/appletgui/SeqCanvas.java
@@
-1,6
+1,6
@@
/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-78,7
+78,7
@@
public class SeqCanvas extends Panel
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);
}
@@
-97,22
+97,22
@@
public class SeqCanvas extends Panel
{
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;
@@
-125,7
+125,7
@@
public class SeqCanvas extends Panel
continue;
}
continue;
}
- value = av.alignment.getSequenceAt(i).findPosition(index);
+ value = av.getAlignment().getSequenceAt(i).findPosition(index);
break;
}
break;
}
@@
-144,16
+144,16
@@
public class SeqCanvas extends Panel
{
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;
@@
-348,9
+348,10
@@
public class SeqCanvas extends Panel
String mask = "0";
int maxWidth = 0;
int tmp;
String mask = "0";
int maxWidth = 0;
int tmp;
- for (int i = 0; i < av.alignment.getHeight(); i++)
+ AlignmentI alignment=av.getAlignment();
+ for (int i = 0; i < alignment.getHeight(); i++)
{
{
- tmp = av.alignment.getSequenceAt(i).getEnd();
+ tmp = alignment.getSequenceAt(i).getEnd();
if (tmp > maxWidth)
{
maxWidth = tmp;
if (tmp > maxWidth)
{
maxWidth = tmp;
@@
-397,9
+398,9
@@
public class SeqCanvas extends Panel
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;
}
@@
-433,7
+434,7
@@
public class SeqCanvas extends Panel
{
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;
@@
-506,7
+507,7
@@
public class SeqCanvas extends Panel
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);
}
@@
-575,14
+576,14
@@
public class SeqCanvas extends Panel
// ///////////////////////////
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)
{
continue;
}
if (nextSeq == null)
{
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)
@@
-619,7
+620,7
@@
public class SeqCanvas extends Panel
}
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);
}
@@
-640,9
+641,9
@@
public class SeqCanvas extends Panel
int ex = -1;
int groupIndex = -1;
int ex = -1;
int groupIndex = -1;
- 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().get(0);
groupIndex = 0;
}
groupIndex = 0;
}
@@
-655,7
+656,7
@@
public class SeqCanvas extends Panel
boolean inGroup = false;
int top = -1;
int bottom = -1;
boolean inGroup = false;
int top = -1;
int bottom = -1;
- int alHeight = av.alignment.getHeight() - 1;
+ int alHeight = av.getAlignment().getHeight() - 1;
for (i = startSeq; i < endSeq; i++)
{
for (i = startSeq; i < endSeq; i++)
{
@@
-670,11
+671,11
@@
public class SeqCanvas extends Panel
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)
&& (i >= alHeight || !group.getSequences(null)
{
if ((bottom == -1)
&& (i >= alHeight || !group.getSequences(null)
- .contains(av.alignment.getSequenceAt(i + 1))))
+ .contains(av.getAlignment().getSequenceAt(i + 1))))
{
bottom = sy + av.charHeight;
}
{
bottom = sy + av.charHeight;
}
@@
-683,7
+684,7
@@
public class SeqCanvas extends Panel
{
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;
}
@@
-793,14
+794,14
@@
public class SeqCanvas extends Panel
groupIndex++;
groupIndex++;
- 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().get(
groupIndex);
groupIndex);
- } while (groupIndex < av.alignment.getGroups().size());
+ } while (groupIndex < av.getAlignment().getGroups().size());
}
}
}
}