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JAL-3931 remove % and - from ids so Pymol doesn’t strip them out and truncate the...
[jalview.git]
/
src
/
jalview
/
commands
/
EditCommand.java
diff --git
a/src/jalview/commands/EditCommand.java
b/src/jalview/commands/EditCommand.java
index
f80bd4a
..
30595bc
100644
(file)
--- a/
src/jalview/commands/EditCommand.java
+++ b/
src/jalview/commands/EditCommand.java
@@
-20,6
+20,8
@@
*/
package jalview.commands;
*/
package jalview.commands;
+import java.util.Locale;
+
import jalview.analysis.AlignSeq;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.analysis.AlignSeq;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
@@
-619,8
+621,8
@@
public class EditCommand implements CommandI
*/
if (command.alIndex[i] < command.al.getHeight())
{
*/
if (command.alIndex[i] < command.al.getHeight())
{
- List<SequenceI> sequences;
- synchronized (sequences = command.al.getSequences())
+ List<SequenceI> sequences = command.al.getSequences();
+ synchronized (sequences)
{
if (!(command.alIndex[i] < 0))
{
{
if (!(command.alIndex[i] < 0))
{
@@
-789,7
+791,7
@@
public class EditCommand implements CommandI
String nogapold = AlignSeq.extractGaps(Comparison.GapChars,
new String(command.string[i]));
String nogapold = AlignSeq.extractGaps(Comparison.GapChars,
new String(command.string[i]));
- if (!nogaprep.toLowerCase().equals(nogapold.toLowerCase()))
+ if (!nogaprep.toLowerCase(Locale.ROOT).equals(nogapold.toLowerCase(Locale.ROOT)))
{
// we may already have dataset and limits stashed...
if (newDSWasNeeded || newStartEndWasNeeded)
{
// we may already have dataset and limits stashed...
if (newDSWasNeeded || newStartEndWasNeeded)
@@
-838,7
+840,7
@@
public class EditCommand implements CommandI
// old ds and edited ds are different, so
// create the new dataset sequence
SequenceI newds = new Sequence(oldds);
// old ds and edited ds are different, so
// create the new dataset sequence
SequenceI newds = new Sequence(oldds);
- newds.setSequence(fullseq);
+ newds.setSequence(fullseq.toUpperCase(Locale.ROOT));
if (command.oldds == null)
{
if (command.oldds == null)
{
@@
-891,7
+893,7
@@
public class EditCommand implements CommandI
// new
// start/end
String nogapalseq = AlignSeq.extractGaps(Comparison.GapChars,
// new
// start/end
String nogapalseq = AlignSeq.extractGaps(Comparison.GapChars,
- command.seqs[i].getSequenceAsString().toUpperCase());
+ command.seqs[i].getSequenceAsString().toUpperCase(Locale.ROOT));
int newStart = command.seqs[i].getDatasetSequence()
.getSequenceAsString().indexOf(nogapalseq);
if (newStart == -1)
int newStart = command.seqs[i].getDatasetSequence()
.getSequenceAsString().indexOf(nogapalseq);
if (newStart == -1)
@@
-1444,45
+1446,51
@@
public class EditCommand implements CommandI
public class Edit
{
public class Edit
{
- private SequenceI[] oldds;
+ SequenceI[] oldds;
/**
* start and end of sequence prior to edit
*/
/**
* start and end of sequence prior to edit
*/
- private Range[] oldStartEnd;
+ Range[] oldStartEnd;
- private boolean fullAlignmentHeight = false;
+ boolean fullAlignmentHeight = false;
- private Map<SequenceI, AlignmentAnnotation[]> deletedAnnotationRows;
+ Map<SequenceI, AlignmentAnnotation[]> deletedAnnotationRows;
- private Map<String, Annotation[]> deletedAnnotations;
+ Map<String, Annotation[]> deletedAnnotations;
/*
* features deleted by the cut (re-add on Undo)
* (including the original of any shortened features)
*/
/*
* features deleted by the cut (re-add on Undo)
* (including the original of any shortened features)
*/
- private Map<SequenceI, List<SequenceFeature>> deletedFeatures;
+ Map<SequenceI, List<SequenceFeature>> deletedFeatures;
/*
* shortened features added by the cut (delete on Undo)
*/
/*
* shortened features added by the cut (delete on Undo)
*/
- private Map<SequenceI, List<SequenceFeature>> truncatedFeatures;
+ Map<SequenceI, List<SequenceFeature>> truncatedFeatures;
- private AlignmentI al;
+ AlignmentI al;
- final private Action command;
+ final Action command;
char[][] string;
SequenceI[] seqs;
char[][] string;
SequenceI[] seqs;
- private int[] alIndex;
+ int[] alIndex;
- private int position;
+ int position;
- private int number;
+ int number;
- private char gapChar;
+ char gapChar;
+
+ /*
+ * flag that identifies edits inserted to balance
+ * user edits in a 'locked editing' region
+ */
+ private boolean systemGenerated;
public Edit(Action cmd, SequenceI[] sqs, int pos, int count,
char gap)
public Edit(Action cmd, SequenceI[] sqs, int pos, int count,
char gap)
@@
-1556,6
+1564,16
@@
public class EditCommand implements CommandI
{
return gapChar;
}
{
return gapChar;
}
+
+ public void setSystemGenerated(boolean b)
+ {
+ systemGenerated = b;
+ }
+
+ public boolean isSystemGenerated()
+ {
+ return systemGenerated;
+ }
}
/**
}
/**