*/
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))
{
public class Edit
{
- private SequenceI[] oldds;
+ SequenceI[] oldds;
/**
* 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)
*/
- private Map<SequenceI, List<SequenceFeature>> deletedFeatures;
+ Map<SequenceI, List<SequenceFeature>> deletedFeatures;
/*
* 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;
- 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