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JAL-2788 possible adjustments to sequence accesses
[jalview.git]
/
src
/
jalview
/
datamodel
/
CigarArray.java
diff --git
a/src/jalview/datamodel/CigarArray.java
b/src/jalview/datamodel/CigarArray.java
index
b6224c2
..
1723f1d
100644
(file)
--- a/
src/jalview/datamodel/CigarArray.java
+++ b/
src/jalview/datamodel/CigarArray.java
@@
-170,32
+170,30
@@
public class CigarArray extends CigarBase
hideStart = region[0];
hideEnd = region[1];
// edit hidden regions to selection range
hideStart = region[0];
hideEnd = region[1];
// edit hidden regions to selection range
- if (hideStart < last)
+
+ // just move on if hideEnd is before last
+ if (hideEnd < last)
{
{
- if (hideEnd > last)
- {
- hideStart = last;
- }
- else
- {
- continue;
- }
+ continue;
}
}
-
+ // exit if next region is after end
if (hideStart > end)
{
break;
}
if (hideStart > end)
{
break;
}
- if (hideEnd > end)
+ // truncate region at start if last falls in region
+ if ((hideStart < last) && (hideEnd >= last))
{
{
- hideEnd = end;
+ hideStart = last;
}
}
- if (hideStart > hideEnd)
+ // truncate region at end if end falls in region
+ if (hideEnd > end) // already checked that hideStart<=end
{
{
- break;
+ hideEnd = end;
}
}
+
/**
* form operations...
*/
/**
* form operations...
*/
@@
-207,7
+205,7
@@
public class CigarArray extends CigarBase
last = hideEnd + 1;
}
// Final match if necessary.
last = hideEnd + 1;
}
// Final match if necessary.
- if (last < end)
+ if (last <= end)
{
addOperation(CigarArray.M, end - last + 1);
}
{
addOperation(CigarArray.M, end - last + 1);
}