git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
JAL-885 more efficient calculation and robust for mismatch between WUSS and alignment...
[jalview.git]
/
src
/
jalview
/
analysis
/
StructureFrequency.java
diff --git
a/src/jalview/analysis/StructureFrequency.java
b/src/jalview/analysis/StructureFrequency.java
index
aa1e277
..
0c9f830
100644
(file)
--- a/
src/jalview/analysis/StructureFrequency.java
+++ b/
src/jalview/analysis/StructureFrequency.java
@@
-122,6
+122,9
@@
public class StructureFrequency
}
else
{
}
else
{
+ bpEnd = findPair(rna, i);
+ if (bpEnd>-1)
+ {
for (j = 0; j < jSize; j++) // foreach row
{
if (sequences[j] == null)
for (j = 0; j < jSize; j++) // foreach row
{
if (sequences[j] == null)
@@
-130,11
+133,8
@@
public class StructureFrequency
.println("WARNING: Consensus skipping null sequence - possible race condition.");
continue;
}
.println("WARNING: Consensus skipping null sequence - possible race condition.");
continue;
}
- seq = sequences[j].getSequence();
-
- if (seq.length > i)
+ c = sequences[j].getCharAt(i);
{
{
- c = seq[i];
// standard representation for gaps in sequence and structure
if (c == '.' || c == ' ')
// standard representation for gaps in sequence and structure
if (c == '.' || c == ' ')
@@
-147,8
+147,7
@@
public class StructureFrequency
values['-']++;
continue;
}
values['-']++;
continue;
}
- bpEnd = findPair(rna, i);
- cEnd = seq[bpEnd];
+ cEnd = sequences[j].getCharAt(bpEnd);
if (checkBpType(c, cEnd))
{
values['(']++; // H means it's a helix (structured)
if (checkBpType(c, cEnd))
{
values['(']++; // H means it's a helix (structured)
@@
-158,6
+157,7
@@
public class StructureFrequency
maxResidue = "(";
}
}
maxResidue = "(";
}
}
+ }
// nonGap++;
}
// UPDATE this for new values
// nonGap++;
}
// UPDATE this for new values