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JAL-1807 explicit imports (jalview.viewmodel)
[jalview.git]
/
src
/
jalview
/
analysis
/
AlignSeq.java
diff --git
a/src/jalview/analysis/AlignSeq.java
b/src/jalview/analysis/AlignSeq.java
index
5612133
..
ed44d4a
100755
(executable)
--- a/
src/jalview/analysis/AlignSeq.java
+++ b/
src/jalview/analysis/AlignSeq.java
@@
-20,13
+20,6
@@
*/
package jalview.analysis;
*/
package jalview.analysis;
-import java.awt.Color;
-import java.awt.Graphics;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-import java.util.StringTokenizer;
-
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Mapping;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Mapping;
@@
-39,6
+32,13
@@
import jalview.util.Format;
import jalview.util.MapList;
import jalview.util.MessageManager;
import jalview.util.MapList;
import jalview.util.MessageManager;
+import java.awt.Color;
+import java.awt.Graphics;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.StringTokenizer;
+
/**
*
*
/**
*
*
@@
-365,8
+365,8
@@
public class AlignSeq
*/
private void SeqInit(String string1, String string2)
{
*/
private void SeqInit(String string1, String string2)
{
- s1str = extractGaps(jalview.util.Comparison.GapChars, string1);
- s2str = extractGaps(jalview.util.Comparison.GapChars, string2);
+ s1str = extractGaps(Comparison.GapChars, string1);
+ s2str = extractGaps(Comparison.GapChars, string2);
if (s1str.length() == 0 || s2str.length() == 0)
{
if (s1str.length() == 0 || s2str.length() == 0)
{
@@
-621,7
+621,7
@@
public class AlignSeq
if ((i + (j * len)) < astr1.length())
{
if (astr1.charAt(i + (j * len)) == astr2.charAt(i + (j * len))
if ((i + (j * len)) < astr1.length())
{
if (astr1.charAt(i + (j * len)) == astr2.charAt(i + (j * len))
- && !jalview.util.Comparison.isGap(astr1.charAt(i
+ && !Comparison.isGap(astr1.charAt(i
+ (j * len))))
{
pid++;
+ (j * len))))
{
pid++;
@@
-664,7
+664,7
@@
public class AlignSeq
pid = pid / (aseq1.length - count) * 100;
output = output.append(new Format("Percentage ID = %2.2f\n\n")
pid = pid / (aseq1.length - count) * 100;
output = output.append(new Format("Percentage ID = %2.2f\n\n")
- .form(pid));
+ .formDouble(pid));
try
{
try
{
@@
-707,7
+707,7
@@
public class AlignSeq
Format.print(System.out, "%3s", s1str.substring(i, i + 1));
}
Format.print(System.out, "%3s", s1str.substring(i, i + 1));
}
- Format.print(System.out, "%3d ", mat[i][j] / 10);
+ Format.printLong(System.out, "%3d ", mat[i][j] / 10);
}
System.out.println();
}
System.out.println();
@@
-1010,7
+1010,7
@@
public class AlignSeq
*
* @return mapping from positions in S1 to corresponding positions in S2
*/
*
* @return mapping from positions in S1 to corresponding positions in S2
*/
- public jalview.datamodel.Mapping getMappingFromS1(boolean allowmismatch)
+ public Mapping getMappingFromS1(boolean allowmismatch)
{
ArrayList<Integer> as1 = new ArrayList<Integer>(), as2 = new ArrayList<Integer>();
int pdbpos = s2.getStart() + getSeq2Start() - 2;
{
ArrayList<Integer> as1 = new ArrayList<Integer>(), as2 = new ArrayList<Integer>();
int pdbpos = s2.getStart() + getSeq2Start() - 2;
@@
-1077,7
+1077,7
@@
public class AlignSeq
}
MapList map = new MapList(mapseq1, mapseq2, 1, 1);
}
MapList map = new MapList(mapseq1, mapseq2, 1, 1);
- jalview.datamodel.Mapping mapping = new Mapping(map);
+ Mapping mapping = new Mapping(map);
mapping.setTo(s2);
return mapping;
}
mapping.setTo(s2);
return mapping;
}