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JAL-2418 source formatting
[jalview.git]
/
src
/
jalview
/
util
/
Comparison.java
diff --git
a/src/jalview/util/Comparison.java
b/src/jalview/util/Comparison.java
index
5269d4f
..
17d3a70
100644
(file)
--- a/
src/jalview/util/Comparison.java
+++ b/
src/jalview/util/Comparison.java
@@
-34,14
+34,15
@@
public class Comparison
private static final int TO_UPPER_CASE = 'a' - 'A';
private static final int TO_UPPER_CASE = 'a' - 'A';
- private static final char GAP_SPACE = ' ';
+ public static final char GAP_SPACE = ' ';
- private static final char GAP_DOT = '.';
+ public static final char GAP_DOT = '.';
- private static final char GAP_DASH = '-';
+ public static final char GAP_DASH = '-';
- public static final String GapChars = new String(new char[] { GAP_SPACE,
- GAP_DOT, GAP_DASH });
+ public static final String GapChars = new String(
+ new char[]
+ { GAP_SPACE, GAP_DOT, GAP_DASH });
/**
* DOCUMENT ME!
/**
* DOCUMENT ME!
@@
-71,7
+72,8
@@
public class Comparison
* int
* @return float
*/
* int
* @return float
*/
- public static float compare(SequenceI ii, SequenceI jj, int start, int end)
+ public static float compare(SequenceI ii, SequenceI jj, int start,
+ int end)
{
String si = ii.getSequenceAsString();
String sj = jj.getSequenceAsString();
{
String si = ii.getSequenceAsString();
String sj = jj.getSequenceAsString();
@@
-97,8
+99,8
@@
public class Comparison
{
for (int j = 0; j < jlen; j++)
{
{
for (int j = 0; j < jlen; j++)
{
- if (si.substring(start + j, start + j + 1).equals(
- sj.substring(start + j, start + j + 1)))
+ if (si.substring(start + j, start + j + 1)
+ .equals(sj.substring(start + j, start + j + 1)))
{
match++;
}
{
match++;
}
@@
-112,8
+114,8
@@
public class Comparison
{
for (int j = 0; j < jlen; j++)
{
{
for (int j = 0; j < jlen; j++)
{
- if (si.substring(start + j, start + j + 1).equals(
- sj.substring(start + j, start + j + 1)))
+ if (si.substring(start + j, start + j + 1)
+ .equals(sj.substring(start + j, start + j + 1)))
{
match++;
}
{
match++;
}
@@
-135,7
+137,9
@@
public class Comparison
* @param s2
* SequenceI
* @return float
* @param s2
* SequenceI
* @return float
+ * @deprecated use PIDModel.computePID()
*/
*/
+ @Deprecated
public final static float PID(String seq1, String seq2)
{
return PID(seq1, seq2, 0, seq1.length());
public final static float PID(String seq1, String seq2)
{
return PID(seq1, seq2, 0, seq1.length());
@@
-144,7
+148,12
@@
public class Comparison
static final int caseShift = 'a' - 'A';
// Another pid with region specification
static final int caseShift = 'a' - 'A';
// Another pid with region specification
- public final static float PID(String seq1, String seq2, int start, int end)
+ /**
+ * @deprecated use PIDModel.computePID()
+ */
+ @Deprecated
+ public final static float PID(String seq1, String seq2, int start,
+ int end)
{
return PID(seq1, seq2, start, end, true, false);
}
{
return PID(seq1, seq2, start, end, true, false);
}
@@
-165,7
+174,9
@@
public class Comparison
* @param ungappedOnly
* - if true - only count PID over ungapped columns
* @return
* @param ungappedOnly
* - if true - only count PID over ungapped columns
* @return
+ * @deprecated use PIDModel.computePID()
*/
*/
+ @Deprecated
public final static float PID(String seq1, String seq2, int start,
int end, boolean wcGaps, boolean ungappedOnly)
{
public final static float PID(String seq1, String seq2, int start,
int end, boolean wcGaps, boolean ungappedOnly)
{
@@
-411,14
+422,14
@@
public class Comparison
flattened.add(s);
}
}
flattened.add(s);
}
}
- final SequenceI[] oneDArray = flattened.toArray(new SequenceI[flattened
- .size()]);
+ final SequenceI[] oneDArray = flattened
+ .toArray(new SequenceI[flattened.size()]);
return isNucleotide(oneDArray);
}
/**
return isNucleotide(oneDArray);
}
/**
- * Compares two chars either case sensitively or case insensitively depending
- * on the caseSensitive flag
+ * Compares two residues either case sensitively or case insensitively
+ * depending on the caseSensitive flag
*
* @param c1
* first char
*
* @param c1
* first char
@@
-428,18
+439,12
@@
public class Comparison
* if true comparison will be case sensitive otherwise its not
* @return
*/
* if true comparison will be case sensitive otherwise its not
* @return
*/
- public static boolean compareChars(char c1, char c2, boolean caseSensitive)
+ public static boolean isSameResidue(char c1, char c2,
+ boolean caseSensitive)
{
{
- boolean sameCase = (Character.isUpperCase(c1) && Character
- .isUpperCase(c2))
- || (Character.isLowerCase(c1) && Character.isLowerCase(c2));
- if (sameCase)
+ if (caseSensitive)
{
{
- return c1 == c2;
- }
- else if (caseSensitive)
- {
- return false;
+ return (c1 == c2);
}
else
{
}
else
{