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JAL-1551 formatting
[jalview.git]
/
src
/
jalview
/
appletgui
/
SequenceRenderer.java
diff --git
a/src/jalview/appletgui/SequenceRenderer.java
b/src/jalview/appletgui/SequenceRenderer.java
index
92d5beb
..
09b50c4
100755
(executable)
--- a/
src/jalview/appletgui/SequenceRenderer.java
+++ b/
src/jalview/appletgui/SequenceRenderer.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-21,7
+21,6
@@
package jalview.appletgui;
import jalview.api.FeatureRenderer;
package jalview.appletgui;
import jalview.api.FeatureRenderer;
-import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.schemes.ColourSchemeI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.schemes.ColourSchemeI;
@@
-161,7
+160,8
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
int length = seq.getLength();
int curStart = -1;
int length = seq.getLength();
int curStart = -1;
- int curWidth = av.charWidth;
+ int curWidth = av.getCharWidth(), avCharWidth = av.getCharWidth(), avCharHeight = av
+ .getCharHeight();
Color tempColour = null;
while (i <= end)
Color tempColour = null;
while (i <= end)
@@
-186,40
+186,41
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
{
if (tempColour != null)
{
{
if (tempColour != null)
{
- graphics.fillRect(av.charWidth * (curStart - start), y1,
- curWidth, av.charHeight);
+ graphics.fillRect(avCharWidth * (curStart - start), y1, curWidth,
+ avCharHeight);
}
graphics.setColor(resBoxColour);
curStart = i;
}
graphics.setColor(resBoxColour);
curStart = i;
- curWidth = av.charWidth;
+ curWidth = avCharWidth;
tempColour = resBoxColour;
}
else
{
tempColour = resBoxColour;
}
else
{
- curWidth += av.charWidth;
+ curWidth += avCharWidth;
}
i++;
}
}
i++;
}
- graphics.fillRect(av.charWidth * (curStart - start), y1, curWidth,
- av.charHeight);
+ graphics.fillRect(avCharWidth * (curStart - start), y1, curWidth,
+ avCharHeight);
}
public void drawText(SequenceI seq, int start, int end, int y1)
{
}
public void drawText(SequenceI seq, int start, int end, int y1)
{
+ int avCharWidth = av.getCharWidth(), avCharHeight = av.getCharHeight();
Font boldFont = null;
boolean bold = false;
Font boldFont = null;
boolean bold = false;
- if (av.upperCasebold)
+ if (av.isUpperCasebold())
{
{
- boldFont = new Font(av.getFont().getName(), Font.BOLD, av.charHeight);
+ boldFont = new Font(av.getFont().getName(), Font.BOLD, avCharHeight);
graphics.setFont(av.getFont());
}
graphics.setFont(av.getFont());
}
- y1 += av.charHeight - av.charHeight / 5; // height/5 replaces pady
+ y1 += avCharHeight - avCharHeight / 5; // height/5 replaces pady
int charOffset = 0;
int charOffset = 0;
@@
-230,7
+231,7
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
}
char s = ' ';
}
char s = ' ';
-
+ boolean srep = av.isDisplayReferenceSeq();
for (int i = start; i <= end; i++)
{
graphics.setColor(Color.black);
for (int i = start; i <= end; i++)
{
graphics.setColor(Color.black);
@@
-255,10
+256,7
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
}
if (currentSequenceGroup.getShowNonconserved())
{
}
if (currentSequenceGroup.getShowNonconserved())
{
- // cheat - use this if we have a consensus for each group: s =
- // getDisplayChar(currentSequenceGroup.getConsensus(), i, s, '.');
- s = getDisplayChar(av.getAlignmentConsensusAnnotation(), i, s,
- '.');
+ s = getDisplayChar(srep, i, s, '.');
}
}
else
}
}
else
@@
-282,13
+280,12
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
}
if (av.getShowUnconserved())
{
}
if (av.getShowUnconserved())
{
- s = getDisplayChar(av.getAlignmentConsensusAnnotation(), i, s,
- '.');
+ s = getDisplayChar(srep, i, s, '.');
}
}
}
}
- if (av.upperCasebold)
+ if (av.isUpperCasebold())
{
fm = graphics.getFontMetrics();
if ('A' <= s && s <= 'Z')
{
fm = graphics.getFontMetrics();
if ('A' <= s && s <= 'Z')
@@
-308,19
+305,23
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
}
}
- charOffset = (av.charWidth - fm.charWidth(s)) / 2;
- graphics.drawString(String.valueOf(s), charOffset + av.charWidth
+ charOffset = (avCharWidth - fm.charWidth(s)) / 2;
+ graphics.drawString(String.valueOf(s), charOffset + avCharWidth
* (i - start), y1);
}
}
* (i - start), y1);
}
}
- private char getDisplayChar(AlignmentAnnotation consensus, int position,
- char s, char c)
+ private char getDisplayChar(final boolean usesrep, int position, char s,
+ char c)
{
{
- char conschar = consensus.annotations[position].displayCharacter
- .charAt(0);
- if (conschar != '-' && s == conschar)
+ // TODO - use currentSequenceGroup rather than alignment
+ // currentSequenceGroup.getConsensus()
+ char conschar = (usesrep) ? av.getAlignment().getSeqrep()
+ .getCharAt(position)
+ : av.getAlignmentConsensusAnnotation().annotations[position].displayCharacter
+ .charAt(0);
+ if (!jalview.util.Comparison.isGap(conschar) && s == conschar)
{
s = c;
}
{
s = c;
}
@@
-350,11
+351,11
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
public void drawHighlightedText(SequenceI seq, int start, int end,
int x1, int y1)
{
public void drawHighlightedText(SequenceI seq, int start, int end,
int x1, int y1)
{
- int pady = av.charHeight / 5;
+ int avCharWidth = av.getCharWidth(), avCharHeight = av.getCharHeight();
+ int pady = avCharHeight / 5;
int charOffset = 0;
graphics.setColor(Color.black);
int charOffset = 0;
graphics.setColor(Color.black);
- graphics.fillRect(x1, y1, av.charWidth * (end - start + 1),
- av.charHeight);
+ graphics.fillRect(x1, y1, avCharWidth * (end - start + 1), avCharHeight);
graphics.setColor(Color.white);
char s = '~';
graphics.setColor(Color.white);
char s = '~';
@@
-368,19
+369,19
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
s = seq.getCharAt(i);
}
s = seq.getCharAt(i);
}
- charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+ charOffset = (avCharWidth - fm.charWidth(s)) / 2;
graphics.drawString(String.valueOf(s), charOffset + x1
graphics.drawString(String.valueOf(s), charOffset + x1
- + av.charWidth * (i - start), y1 + av.charHeight - pady);
+ + avCharWidth * (i - start), y1 + avCharHeight - pady);
}
}
}
public void drawCursor(SequenceI seq, int res, int x1, int y1)
{
}
}
}
public void drawCursor(SequenceI seq, int res, int x1, int y1)
{
- int pady = av.charHeight / 5;
+ int pady = av.getCharHeight() / 5;
int charOffset = 0;
graphics.setColor(Color.black);
int charOffset = 0;
graphics.setColor(Color.black);
- graphics.fillRect(x1, y1, av.charWidth, av.charHeight);
+ graphics.fillRect(x1, y1, av.getCharWidth(), av.getCharHeight());
graphics.setColor(Color.white);
graphics.setColor(Color.white);
graphics.setColor(Color.white);
graphics.setColor(Color.white);
@@
-389,9
+390,9
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
if (av.validCharWidth)
{
if (av.validCharWidth)
{
- charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+ charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2;
graphics.drawString(String.valueOf(s), charOffset + x1,
graphics.drawString(String.valueOf(s), charOffset + x1,
- (y1 + av.charHeight) - pady);
+ (y1 + av.getCharHeight()) - pady);
}
}
}
}