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JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob
[jalview.git]
/
src
/
jalview
/
analysis
/
AAFrequency.java
diff --git
a/src/jalview/analysis/AAFrequency.java
b/src/jalview/analysis/AAFrequency.java
index
50045dc
..
3a79959
100755
(executable)
--- a/
src/jalview/analysis/AAFrequency.java
+++ b/
src/jalview/analysis/AAFrequency.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-198,9
+198,8
@@
public class AAFrequency
if (profile)
{
// TODO use a 1-dimensional array with jSize, nongap in [0] and [1]
if (profile)
{
// TODO use a 1-dimensional array with jSize, nongap in [0] and [1]
- residueHash.put(PROFILE, new int[][]
- { values, new int[]
- { jSize, nongap } });
+ residueHash.put(PROFILE, new int[][] { values,
+ new int[] { jSize, nongap } });
}
residueHash.put(MAXCOUNT, new Integer(maxCount));
residueHash.put(MAXRESIDUE, maxResidue);
}
residueHash.put(MAXCOUNT, new Integer(maxCount));
residueHash.put(MAXRESIDUE, maxResidue);
@@
-369,8
+368,7
@@
public class AAFrequency
.append("%");
}
consensus.annotations[i] = new Annotation(maxRes,
.append("%");
}
consensus.annotations[i] = new Annotation(maxRes,
- mouseOver.toString(), ' ',
- value);
+ mouseOver.toString(), ' ', value);
}
}
}
}
@@
-462,7
+460,8
@@
public class AAFrequency
* @param hashtable
* @return
*/
* @param hashtable
* @return
*/
- public static int[] extractCdnaProfile(Hashtable hashtable, boolean ignoreGaps)
+ public static int[] extractCdnaProfile(Hashtable 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
@@
-507,7
+506,7
@@
public class AAFrequency
result[1] = distinctValuesCount;
return Arrays.copyOfRange(result, 0, j);
}
result[1] = distinctValuesCount;
return Arrays.copyOfRange(result, 0, j);
}
-
+
/**
* Compute a consensus for the cDNA coding for a protein alignment.
*
/**
* Compute a consensus for the cDNA coding for a protein alignment.
*
@@
-664,8
+663,7
@@
public class AAFrequency
final int pct = codonCount * 100 / totalCount;
String codon = String
.valueOf(CodingUtils.decodeCodon(codonEncoded));
final int pct = codonCount * 100 / totalCount;
String codon = String
.valueOf(CodingUtils.decodeCodon(codonEncoded));
- percent = fmt == null ? Integer.toString(pct) : fmt
- .form(pct);
+ percent = fmt == null ? Integer.toString(pct) : fmt.form(pct);
if (showProfileLogo || codonCount == modalCodonCount)
{
if (percent.equals(lastPercent) && j > 0)
if (showProfileLogo || codonCount == modalCodonCount)
{
if (percent.equals(lastPercent) && j > 0)
@@
-678,8
+676,7
@@
public class AAFrequency
if (samePercent.length() > 0)
{
mouseOver.append(samePercent).append(": ")
if (samePercent.length() > 0)
{
mouseOver.append(samePercent).append(": ")
- .append(lastPercent)
- .append("% ");
+ .append(lastPercent).append("% ");
}
samePercent.setLength(0);
samePercent.append(codon);
}
samePercent.setLength(0);
samePercent.append(codon);