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Merge branch 'patch/VAqua_saveload_update_JAL-2988' into releases/Release_2_10_5_Branch
[jalview.git]
/
src
/
jalview
/
analysis
/
StructureFrequency.java
diff --git
a/src/jalview/analysis/StructureFrequency.java
b/src/jalview/analysis/StructureFrequency.java
index
7b0858d
..
b681aa6
100644
(file)
--- a/
src/jalview/analysis/StructureFrequency.java
+++ b/
src/jalview/analysis/StructureFrequency.java
@@
-149,8
+149,8
@@
public class StructureFrequency
{
if (sequences[j] == null)
{
{
if (sequences[j] == null)
{
- System.err
- .println("WARNING: Consensus skipping null sequence - possible race condition.");
+ System.err.println(
+ "WARNING: Consensus skipping null sequence - possible race condition.");
continue;
}
continue;
}
@@
-195,8
+195,9
@@
public class StructureFrequency
if (profile)
{
// TODO 1-dim array with jsize in [0], nongapped in [1]; or Pojo
if (profile)
{
// TODO 1-dim array with jsize in [0], nongapped in [1]; or Pojo
- residueHash.put(PROFILE, new int[][] { values,
- new int[] { jSize, (jSize - values['-']) } });
+ residueHash.put(PROFILE,
+ new int[][]
+ { values, new int[] { jSize, (jSize - values['-']) } });
residueHash.put(PAIRPROFILE, pairs);
}
residueHash.put(PAIRPROFILE, pairs);
}
@@
-217,7
+218,8
@@
public class StructureFrequency
{
if (canonicalOrWobblePairCount >= otherPairCount)
{
{
if (canonicalOrWobblePairCount >= otherPairCount)
{
- maxResidue = (canonicalOrWobblePairCount - canonical) < canonical ? "("
+ maxResidue = (canonicalOrWobblePairCount - canonical) < canonical
+ ? "("
: "[";
}
else
: "[";
}
else
@@
-252,8
+254,9
@@
public class StructureFrequency
residueHash = new Hashtable();
if (profile)
{
residueHash = new Hashtable();
if (profile)
{
- residueHash.put(PROFILE, new int[][] { values,
- new int[] { jSize, (jSize - values['-']) } });
+ residueHash.put(PROFILE,
+ new int[][]
+ { values, new int[] { jSize, (jSize - values['-']) } });
residueHash.put(PAIRPROFILE, pairs);
}
residueHash.put(PAIRPROFILE, pairs);
}
@@
-444,7
+447,8
@@
public class StructureFrequency
int valuesCount = 0;
rtnval[1] = 0;
int offset = 2;
int valuesCount = 0;
rtnval[1] = 0;
int offset = 2;
- final int divisor = profile[1][ignoreGapsInConsensusCalculation ? 1 : 0];
+ final int divisor = profile[1][ignoreGapsInConsensusCalculation ? 1
+ : 0];
for (int c = 624; c > 0; c--)
{
if (vl[c] > 0)
for (int c = 624; c > 0; c--)
{
if (vl[c] > 0)