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JAL-4001 Check --nousagestats before doing analytics in headless mode
[jalview.git]
/
src
/
jalview
/
analysis
/
AAFrequency.java
diff --git
a/src/jalview/analysis/AAFrequency.java
b/src/jalview/analysis/AAFrequency.java
index
61f3b7f
..
b1505d6
100755
(executable)
--- a/
src/jalview/analysis/AAFrequency.java
+++ b/
src/jalview/analysis/AAFrequency.java
@@
-483,8
+483,7
@@
public class AAFrequency
* @return
*/
public static int[] extractCdnaProfile(
* @return
*/
public static int[] extractCdnaProfile(
- Hashtable<String, Object> hashtable,
- boolean ignoreGaps)
+ Hashtable<String, Object> hashtable, boolean ignoreGaps)
{
// this holds #seqs, #ungapped, and then codon count, indexed by encoded
// codon triplet
{
// this holds #seqs, #ungapped, and then codon count, indexed by encoded
// codon triplet
@@
-580,6
+579,7
@@
public class AAFrequency
{
codonCounts[codonEncoded + 2]++;
ungappedCount++;
{
codonCounts[codonEncoded + 2]++;
ungappedCount++;
+ break;
}
}
}
}
}
}
@@
-605,8
+605,8
@@
public class AAFrequency
*/
public static void completeCdnaConsensus(
AlignmentAnnotation consensusAnnotation,
*/
public static void completeCdnaConsensus(
AlignmentAnnotation consensusAnnotation,
- Hashtable<String, Object>[] consensusData, boolean showProfileLogo,
- int nseqs)
+ Hashtable<String, Object>[] consensusData,
+ boolean showProfileLogo, int nseqs)
{
if (consensusAnnotation == null
|| consensusAnnotation.annotations == null
{
if (consensusAnnotation == null
|| consensusAnnotation.annotations == null