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Use the isGap method in utils
author
amwaterhouse
<Andrew Waterhouse>
Fri, 17 Dec 2004 14:18:13 +0000
(14:18 +0000)
committer
amwaterhouse
<Andrew Waterhouse>
Fri, 17 Dec 2004 14:18:13 +0000
(14:18 +0000)
src/jalview/datamodel/Alignment.java
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src/jalview/gui/AlignFrame.java
patch
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src/jalview/gui/ScorePanel.java
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src/jalview/gui/SequenceRenderer.java
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diff --git
a/src/jalview/datamodel/Alignment.java
b/src/jalview/datamodel/Alignment.java
index
3fa1379
..
f480f0f
100755
(executable)
--- a/
src/jalview/datamodel/Alignment.java
+++ b/
src/jalview/datamodel/Alignment.java
@@
-112,7
+112,7
@@
public class Alignment implements AlignmentI
if (current.getLength() > i)
\r
{
\r
/* MC Should move this to a method somewhere */
\r
if (current.getLength() > i)
\r
{
\r
/* MC Should move this to a method somewhere */
\r
- if (current.getCharAt(i)!='-' && current.getCharAt(i)!='.' && current.getCharAt(i)!=' ')
\r
+ if ( !jalview.util.Comparison.isGap(current.getCharAt(i)))
\r
delete = false;
\r
\r
}
\r
delete = false;
\r
\r
}
\r
@@
-385,12
+385,14
@@
public class Alignment implements AlignmentI
}
\r
\r
/** */
\r
}
\r
\r
/** */
\r
- public int findIndex(SequenceI s) {
\r
+ public int findIndex(SequenceI s)
\r
+ {
\r
int i=0;
\r
int i=0;
\r
- while (i < sequences.size()) {
\r
- if (s == getSequenceAt(i)) {
\r
+ while (i < sequences.size())
\r
+ {
\r
+ if (s == getSequenceAt(i))
\r
return i;
\r
return i;
\r
- }
\r
+
\r
i++;
\r
}
\r
return -1;
\r
i++;
\r
}
\r
return -1;
\r
diff --git
a/src/jalview/gui/AlignFrame.java
b/src/jalview/gui/AlignFrame.java
index
7feadb9
..
c0216aa
100755
(executable)
--- a/
src/jalview/gui/AlignFrame.java
+++ b/
src/jalview/gui/AlignFrame.java
@@
-280,7
+280,7
@@
public class AlignFrame extends GAlignFrame
current = viewport.getAlignment().getSequenceAt(i);
\r
jSize = current.getLength();
\r
for (int j=0; j < jSize; j++)
\r
current = viewport.getAlignment().getSequenceAt(i);
\r
jSize = current.getLength();
\r
for (int j=0; j < jSize; j++)
\r
- if (current.getCharAt(j)=='-' || current.getCharAt(j)=='.' || current.getCharAt(j)==' ')
\r
+ if(jalview.util.Comparison.isGap(current.getCharAt(i)))
\r
{
\r
current.deleteCharAt(j);
\r
j--;
\r
{
\r
current.deleteCharAt(j);
\r
j--;
\r
diff --git
a/src/jalview/gui/ScorePanel.java
b/src/jalview/gui/ScorePanel.java
index
b4bb3c9
..
e6ba4b3
100755
(executable)
--- a/
src/jalview/gui/ScorePanel.java
+++ b/
src/jalview/gui/ScorePanel.java
@@
-92,7
+92,7
@@
public class ScorePanel extends JPanel
value = (int) ( (float) value /
\r
Float.parseFloat(hash.get("size").toString()) * 55);
\r
\r
value = (int) ( (float) value /
\r
Float.parseFloat(hash.get("size").toString()) * 55);
\r
\r
- if (character != ' ' && character != '.' && character != '-')
\r
+ if ( !jalview.util.Comparison.isGap(character))
\r
g.fillRect( (int) (i * av.charWidth),
\r
60 - value,
\r
(int) av.charWidth,
\r
g.fillRect( (int) (i * av.charWidth),
\r
60 - value,
\r
(int) av.charWidth,
\r
diff --git
a/src/jalview/gui/SequenceRenderer.java
b/src/jalview/gui/SequenceRenderer.java
index
82124ce
..
5022050
100755
(executable)
--- a/
src/jalview/gui/SequenceRenderer.java
+++ b/
src/jalview/gui/SequenceRenderer.java
@@
-101,7
+101,7
@@
try{
else
\r
s = ' ';
\r
\r
else
\r
s = ' ';
\r
\r
- if(!renderGaps && (s=='-' || s=='.' || s==' '))
\r
+ if(!renderGaps && jalview.util.Comparison.isGap(s))
\r
continue;
\r
\r
g.setColor(Color.black);
\r
continue;
\r
\r
g.setColor(Color.black);
\r