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JAL-4390 don't output alignment to text panel and stdout when lots of sequences proce...
[jalview.git]
/
src
/
jalview
/
datamodel
/
ResidueCount.java
diff --git
a/src/jalview/datamodel/ResidueCount.java
b/src/jalview/datamodel/ResidueCount.java
index
3e3a966
..
dc98f99
100644
(file)
--- a/
src/jalview/datamodel/ResidueCount.java
+++ b/
src/jalview/datamodel/ResidueCount.java
@@
-28,6
+28,7
@@
import jalview.util.SparseCount;
/**
* A class to count occurrences of residues in a profile, optimised for speed
* and memory footprint.
/**
* A class to count occurrences of residues in a profile, optimised for speed
* and memory footprint.
+ *
* @author gmcarstairs
*
*/
* @author gmcarstairs
*
*/
@@
-69,7
+70,7
@@
public class ResidueCount
*/
private static final String AAS = "ACDEFGHIKLMNPQRSTUVWXY";
*/
private static final String AAS = "ACDEFGHIKLMNPQRSTUVWXY";
- private static final int GAP_COUNT = 0;
+ static final int GAP_COUNT = 0;
/*
* fast lookup tables holding the index into our count
/*
* fast lookup tables holding the index into our count
@@
-211,7
+212,12
@@
public class ResidueCount
counts[offset] = (short) ++newValue;
}
}
counts[offset] = (short) ++newValue;
}
}
- maxCount = Math.max(maxCount, newValue);
+
+ if (offset != GAP_COUNT)
+ {
+ // update modal residue count
+ maxCount = Math.max(maxCount, newValue);
+ }
return newValue;
}
return newValue;
}
@@
-300,15
+306,7
@@
public class ResidueCount
*/
public int addGap()
{
*/
public int addGap()
{
- int newValue;
- if (useIntCounts)
- {
- newValue = ++intCounts[GAP_COUNT];
- }
- else
- {
- newValue = ++counts[GAP_COUNT];
- }
+ int newValue = increment(GAP_COUNT);
return newValue;
}
return newValue;
}
@@
-447,8
+445,8
@@
public class ResidueCount
{
if (intCounts[i] == count)
{
{
if (intCounts[i] == count)
{
- modal.append(isNucleotide ? NUCS.charAt(i - 1) : AAS
- .charAt(i - 1));
+ modal.append(
+ isNucleotide ? NUCS.charAt(i - 1) : AAS.charAt(i - 1));
}
}
}
}
}
}
@@
-458,8
+456,8
@@
public class ResidueCount
{
if (counts[i] == count)
{
{
if (counts[i] == count)
{
- modal.append(isNucleotide ? NUCS.charAt(i - 1) : AAS
- .charAt(i - 1));
+ modal.append(
+ isNucleotide ? NUCS.charAt(i - 1) : AAS.charAt(i - 1));
}
}
}
}
}
}
@@
-492,7
+490,8
@@
public class ResidueCount
*
* @return
*/
*
* @return
*/
- public int size() {
+ public int size()
+ {
int size = 0;
if (useIntCounts)
{
int size = 0;
if (useIntCounts)
{
@@
-546,8
+545,8
@@
public class ResidueCount
{
if (intCounts[i] > 0)
{
{
if (intCounts[i] > 0)
{
- char symbol = isNucleotide ? NUCS.charAt(i - 1) : AAS
- .charAt(i - 1);
+ char symbol = isNucleotide ? NUCS.charAt(i - 1)
+ : AAS.charAt(i - 1);
symbols[j] = symbol;
values[j] = intCounts[i];
j++;
symbols[j] = symbol;
values[j] = intCounts[i];
j++;
@@
-560,8
+559,8
@@
public class ResidueCount
{
if (counts[i] > 0)
{
{
if (counts[i] > 0)
{
- char symbol = isNucleotide ? NUCS.charAt(i - 1) : AAS
- .charAt(i - 1);
+ char symbol = isNucleotide ? NUCS.charAt(i - 1)
+ : AAS.charAt(i - 1);
symbols[j] = symbol;
values[j] = counts[i];
j++;
symbols[j] = symbol;
values[j] = counts[i];
j++;