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RefreshPanels after a colour change
[jalview.git]
/
src
/
jalview
/
datamodel
/
Sequence.java
diff --git
a/src/jalview/datamodel/Sequence.java
b/src/jalview/datamodel/Sequence.java
index
cc5d760
..
d35cbe8
100755
(executable)
--- a/
src/jalview/datamodel/Sequence.java
+++ b/
src/jalview/datamodel/Sequence.java
@@
-144,19
+144,18
@@
public class Sequence implements SequenceI
\r
while (i< sequence.length() && j <= end && j <= pos) {
\r
\r
\r
while (i< sequence.length() && j <= end && j <= pos) {
\r
\r
- String s = sequence.substring(i,i+1);
\r
+ char c = sequence.charAt(i);
\r
\r
\r
- if (!(s.equals(".") || s.equals("-") || s.equals(" "))) {
\r
+ if (!jalview.util.Comparison.isGap((c)))
\r
j++;
\r
j++;
\r
- }
\r
+
\r
i++;
\r
}
\r
i++;
\r
}
\r
- if (j == end && j < pos) {
\r
+ if (j == end && j < pos)
\r
return end+1;
\r
return end+1;
\r
- } else {
\r
-
\r
+ else
\r
return i;
\r
return i;
\r
- }
\r
+
\r
}
\r
\r
public int findPosition(int i) {
\r
}
\r
\r
public int findPosition(int i) {
\r
@@
-164,12
+163,13
@@
public class Sequence implements SequenceI
int j = 0;
\r
int pos = start;
\r
\r
int j = 0;
\r
int pos = start;
\r
\r
- while (j < i) {
\r
- String s = sequence.substring(j,j+1);
\r
+ while (j < i)
\r
+ {
\r
+ char c = sequence.charAt(j);
\r
\r
\r
- if (!(s.equals(".") || s.equals("-") || s.equals(" "))) {
\r
+ if (!jalview.util.Comparison.isGap((c)))
\r
pos++;
\r
pos++;
\r
- }
\r
+
\r
j++;
\r
}
\r
return pos;
\r
j++;
\r
}
\r
return pos;
\r