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JAL-4290 new CommandsTest.headlessOrGuiImageOutputTest - uses CommandLineOperations...
[jalview.git]
/
src
/
jalview
/
commands
/
ChangeCaseCommand.java
diff --git
a/src/jalview/commands/ChangeCaseCommand.java
b/src/jalview/commands/ChangeCaseCommand.java
index
1114ce9
..
1476768
100644
(file)
--- a/
src/jalview/commands/ChangeCaseCommand.java
+++ b/
src/jalview/commands/ChangeCaseCommand.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-20,7
+20,12
@@
*/
package jalview.commands;
*/
package jalview.commands;
-import jalview.datamodel.*;
+import java.util.Locale;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+
+import java.util.List;
public class ChangeCaseCommand implements CommandI
{
public class ChangeCaseCommand implements CommandI
{
@@
-36,10
+41,10
@@
public class ChangeCaseCommand implements CommandI
SequenceI[] seqs;
SequenceI[] seqs;
- int[][] regions;
+ List<int[]> regions;
public ChangeCaseCommand(String description, SequenceI[] seqs,
public ChangeCaseCommand(String description, SequenceI[] seqs,
- int[][] regions, int caseChange)
+ List<int[]> regions, int caseChange)
{
this.description = description;
this.seqs = seqs;
{
this.description = description;
this.seqs = seqs;
@@
-73,21
+78,21
@@
public class ChangeCaseCommand implements CommandI
String sequence;
int start, end;
char nextChar;
String sequence;
int start, end;
char nextChar;
- for (int r = 0; r < regions.length; r++)
+ for (int[] r : regions)
{
{
- start = regions[r][0];
+ start = r[0];
for (int s = 0; s < seqs.length; s++)
{
sequence = seqs[s].getSequenceAsString();
StringBuffer newSeq = new StringBuffer();
for (int s = 0; s < seqs.length; s++)
{
sequence = seqs[s].getSequenceAsString();
StringBuffer newSeq = new StringBuffer();
- if (regions[r][1] > sequence.length())
+ if (r[1] > sequence.length())
{
end = sequence.length();
}
else
{
{
end = sequence.length();
}
else
{
- end = regions[r][1];
+ end = r[1];
}
if (start > 0)
}
if (start > 0)
@@
-98,13
+103,15
@@
public class ChangeCaseCommand implements CommandI
if ((caseChange == TO_UPPER && doCommand)
|| (caseChange == TO_LOWER && !doCommand))
{
if ((caseChange == TO_UPPER && doCommand)
|| (caseChange == TO_LOWER && !doCommand))
{
- newSeq.append(sequence.substring(start, end).toUpperCase());
+ newSeq.append(
+ sequence.substring(start, end).toUpperCase(Locale.ROOT));
}
else if ((caseChange == TO_LOWER && doCommand)
|| (caseChange == TO_UPPER && !doCommand))
{
}
else if ((caseChange == TO_LOWER && doCommand)
|| (caseChange == TO_UPPER && !doCommand))
{
- newSeq.append(sequence.substring(start, end).toLowerCase());
+ newSeq.append(
+ sequence.substring(start, end).toLowerCase(Locale.ROOT));
}
else
}
else