X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcommands%2FEditCommand.java;h=30595bce2afcec658ce343e5ee7067bcd3310c03;hb=41b0e9331ac71787c1280aa1d809f54c575fbf97;hp=894dc754bbc23298c4fd71ac8f208e1370c82e2e;hpb=f7b3f09efa23c9353afee3ad7f57c61ab2560e41;p=jalview.git diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java index 894dc75..30595bc 100644 --- a/src/jalview/commands/EditCommand.java +++ b/src/jalview/commands/EditCommand.java @@ -20,10 +20,13 @@ */ package jalview.commands; +import java.util.Locale; + import jalview.analysis.AlignSeq; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.Annotation; +import jalview.datamodel.ContiguousI; import jalview.datamodel.Range; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceFeature; @@ -118,7 +121,7 @@ public class EditCommand implements CommandI public abstract Action getUndoAction(); }; - private List edits = new ArrayList(); + private List edits = new ArrayList<>(); String description; @@ -526,13 +529,8 @@ public class EditCommand implements CommandI command.string[i] = sequence.getSequence(command.position, command.position + command.number); SequenceI oldds = sequence.getDatasetSequence(); - if (command.oldds != null && command.oldds[i] != null) - { - // we are redoing an undone cut. - sequence.setDatasetSequence(null); - } - Range cutPositions = sequence.findPositions(command.position + 1, - command.position + command.number); + ContiguousI cutPositions = sequence.findPositions( + command.position + 1, command.position + command.number); boolean cutIsInternal = cutPositions != null && sequence.getStart() != cutPositions .getBegin() && sequence.getEnd() != cutPositions.getEnd(); @@ -544,27 +542,23 @@ public class EditCommand implements CommandI SequenceI ds = sequence.getDatasetSequence(); sequence.deleteChars(command.position, command.position + command.number); - SequenceI newDs = sequence.getDatasetSequence(); - if (newDs != ds && command.al != null - && command.al.getDataset() != null - && !command.al.getDataset().getSequences().contains(newDs)) - { - command.al.getDataset().addSequence(newDs); - } if (command.oldds != null && command.oldds[i] != null) { - // Undoing previous Paste - so - // oldds entry contains the cut dataset sequence, - // with sequence features in expected place. + /* + * we are Redoing a Cut, or Undoing a Paste - so + * oldds entry contains the cut dataset sequence, + * with sequence features in expected place + */ sequence.setDatasetSequence(command.oldds[i]); command.oldds[i] = oldds; } else { - // New cut operation - // We always keep track of the dataset sequence so we can safely - // restore it during the Undo + /* + * new cut operation: save the dataset sequence + * so it can be restored in an Undo + */ if (command.oldds == null) { command.oldds = new SequenceI[command.seqs.length]; @@ -584,6 +578,13 @@ public class EditCommand implements CommandI } } } + SequenceI newDs = sequence.getDatasetSequence(); + if (newDs != ds && command.al != null + && command.al.getDataset() != null + && !command.al.getDataset().getSequences().contains(newDs)) + { + command.al.getDataset().addSequence(newDs); + } } if (sequence.getLength() < 1) @@ -620,8 +621,8 @@ public class EditCommand implements CommandI */ if (command.alIndex[i] < command.al.getHeight()) { - List sequences; - synchronized (sequences = command.al.getSequences()) + List sequences = command.al.getSequences(); + synchronized (sequences) { if (!(command.alIndex[i] < 0)) { @@ -720,6 +721,12 @@ public class EditCommand implements CommandI command.oldds[i] = sequence.getDatasetSequence(); sameDatasetSequence = ds == sequence.getDatasetSequence(); ds.setSequenceFeatures(sequence.getSequenceFeatures()); + if (!sameDatasetSequence && command.al.getDataset() != null) + { + // delete 'undone' sequence from alignment dataset + command.al.getDataset() + .deleteSequence(sequence.getDatasetSequence()); + } sequence.setDatasetSequence(ds); } undoCutFeatures(command, command.seqs[i], start, length, @@ -733,7 +740,7 @@ public class EditCommand implements CommandI static void replace(Edit command) { - StringBuffer tmp; + StringBuilder tmp; String oldstring; int start = command.position; int end = command.number; @@ -759,19 +766,16 @@ public class EditCommand implements CommandI * EditCommand.PASTE, sequences, 0, alignment.getWidth(), alignment) ); * */ - - Range beforeEditedPositions = command.seqs[i].findPositions(1, start); - Range afterEditedPositions = command.seqs[i] - .findPositions(start + end + 1, command.seqs[i].getLength()); + ContiguousI beforeEditedPositions = command.seqs[i].findPositions(1, + start); + ContiguousI afterEditedPositions = command.seqs[i] + .findPositions(end + 1, command.seqs[i].getLength()); oldstring = command.seqs[i].getSequenceAsString(); - tmp = new StringBuffer(oldstring.substring(0, start)); + tmp = new StringBuilder(oldstring.substring(0, start)); tmp.append(command.string[i]); - String nogaprep = jalview.analysis.AlignSeq.extractGaps( - jalview.util.Comparison.GapChars, + String nogaprep = AlignSeq.extractGaps(Comparison.GapChars, new String(command.string[i])); - int ipos = command.seqs[i].findPosition(start) - - command.seqs[i].getStart(); if (end < oldstring.length()) { tmp.append(oldstring.substring(end)); @@ -787,7 +791,7 @@ public class EditCommand implements CommandI 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) @@ -813,9 +817,22 @@ public class EditCommand implements CommandI // first edit the original dataset sequence string SequenceI oldds = command.seqs[i].getDatasetSequence(); String osp = oldds.getSequenceAsString(); - - String fullseq = osp.substring(0, ipos) + nogaprep - + osp.substring(ipos + nogaprep.length()); + int beforeStartOfEdit = -oldds.getStart() + 1 + + (beforeEditedPositions == null + ? ((afterEditedPositions != null) + ? afterEditedPositions.getBegin() - 1 + : oldstartend.getBegin() + + nogapold.length()) + : beforeEditedPositions.getEnd() + ); + int afterEndOfEdit = -oldds.getStart() + 1 + + ((afterEditedPositions == null) + ? oldstartend.getEnd() + : afterEditedPositions.getBegin() - 1); + String fullseq = osp.substring(0, + beforeStartOfEdit) + + nogaprep + + osp.substring(afterEndOfEdit); // and check if new sequence data is different.. if (!fullseq.equalsIgnoreCase(osp)) @@ -823,13 +840,21 @@ public class EditCommand implements CommandI // old ds and edited ds are different, so // create the new dataset sequence SequenceI newds = new Sequence(oldds); - newds.setSequence(fullseq.toUpperCase()); + newds.setSequence(fullseq.toUpperCase(Locale.ROOT)); if (command.oldds == null) { command.oldds = new SequenceI[command.seqs.length]; } command.oldds[i] = command.seqs[i].getDatasetSequence(); + + // And preserve start/end for good-measure + + if (command.oldStartEnd == null) + { + command.oldStartEnd = new Range[command.seqs.length]; + } + command.oldStartEnd[i] = oldstartend; // TODO: JAL-1131 ensure newly created dataset sequence is added to // the set of // dataset sequences associated with the alignment. @@ -867,9 +892,8 @@ public class EditCommand implements CommandI // edit covered both start and end. Here we can only guess the // new // start/end - String nogapalseq = jalview.analysis.AlignSeq.extractGaps( - jalview.util.Comparison.GapChars, - command.seqs[i].getSequenceAsString().toUpperCase()); + String nogapalseq = AlignSeq.extractGaps(Comparison.GapChars, + command.seqs[i].getSequenceAsString().toUpperCase(Locale.ROOT)); int newStart = command.seqs[i].getDatasetSequence() .getSequenceAsString().indexOf(nogapalseq); if (newStart == -1) @@ -898,7 +922,7 @@ public class EditCommand implements CommandI if (modifyVisibility && !insert) { // only occurs if a sequence was added or deleted. - command.deletedAnnotationRows = new Hashtable(); + command.deletedAnnotationRows = new Hashtable<>(); } if (command.fullAlignmentHeight) { @@ -1056,7 +1080,7 @@ public class EditCommand implements CommandI if (!insert) { - command.deletedAnnotations = new Hashtable(); + command.deletedAnnotations = new Hashtable<>(); } int aSize; @@ -1340,7 +1364,7 @@ public class EditCommand implements CommandI */ public Map priorState(boolean forUndo) { - Map result = new HashMap(); + Map result = new HashMap<>(); if (getEdits() == null) { return result; @@ -1373,7 +1397,7 @@ public class EditCommand implements CommandI * Work backwards through the edit list, deriving the sequences before each * was applied. The final result is the sequence set before any edits. */ - Iterator editList = new ReverseListIterator(getEdits()); + Iterator editList = new ReverseListIterator<>(getEdits()); while (editList.hasNext()) { Edit oldEdit = editList.next(); @@ -1422,45 +1446,51 @@ public class EditCommand implements CommandI 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 deletedAnnotationRows; + Map deletedAnnotationRows; - private Map deletedAnnotations; + Map deletedAnnotations; /* * features deleted by the cut (re-add on Undo) * (including the original of any shortened features) */ - private Map> deletedFeatures; + Map> deletedFeatures; /* * shortened features added by the cut (delete on Undo) */ - private Map> truncatedFeatures; + Map> 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 + * user edits in a 'locked editing' region + */ + private boolean systemGenerated; public Edit(Action cmd, SequenceI[] sqs, int pos, int count, char gap) @@ -1534,6 +1564,16 @@ public class EditCommand implements CommandI { return gapChar; } + + public void setSystemGenerated(boolean b) + { + systemGenerated = b; + } + + public boolean isSystemGenerated() + { + return systemGenerated; + } } /** @@ -1551,7 +1591,7 @@ public class EditCommand implements CommandI } else { - return new ReverseListIterator(getEdits()); + return new ReverseListIterator<>(getEdits()); } }