X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcommands%2FEditCommand.java;h=b9d32f79d5adc1c777e418056da131a5dcf94ed6;hb=c793942b6430bba9d9b6795e4afd8a1907c022d7;hp=f71fb79070ae9c357443429ad447fde756b1c67c;hpb=51c792ab859d3979c966678f2fed8e1103b43d78;p=jalview.git diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java index f71fb79..b9d32f7 100644 --- a/src/jalview/commands/EditCommand.java +++ b/src/jalview/commands/EditCommand.java @@ -24,6 +24,7 @@ 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 +119,7 @@ public class EditCommand implements CommandI public abstract Action getUndoAction(); }; - private List edits = new ArrayList(); + private List edits = new ArrayList<>(); String description; @@ -526,13 +527,8 @@ 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 +540,23 @@ 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 +576,13 @@ 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) @@ -720,6 +719,12 @@ 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 +738,7 @@ public class EditCommand implements CommandI static void replace(Edit command) { - StringBuffer tmp; + StringBuilder tmp; String oldstring; int start = command.position; int end = command.number; @@ -759,23 +764,24 @@ 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)); } + // stash end prior to updating the sequence object so we can save it if + // need be. + Range oldstartend = new Range(command.seqs[i].getStart(), + command.seqs[i].getEnd()); command.seqs[i].setSequence(tmp.toString()); command.string[i] = oldstring .substring(start, Math.min(end, oldstring.length())) @@ -785,31 +791,46 @@ public class EditCommand implements CommandI if (!nogaprep.toLowerCase().equals(nogapold.toLowerCase())) { - // probably need a new dataset sequence - if (newDSWasNeeded) + // we may already have dataset and limits stashed... + if (newDSWasNeeded || newStartEndWasNeeded) { + if (newDSWasNeeded) + { // then just switch the dataset sequence SequenceI oldds = command.seqs[i].getDatasetSequence(); command.seqs[i].setDatasetSequence(command.oldds[i]); command.oldds[i] = oldds; - } - else - if (newStartEndWasNeeded) - { - Range newStart = command.oldStartEnd[i]; - command.oldStartEnd[i] = new Range(command.seqs[i].getStart(), - command.seqs[i].getEnd()); - command.seqs[i].setStart(newStart.getBegin()); - command.seqs[i].setEnd(newStart.getEnd()); + } + if (newStartEndWasNeeded) + { + Range newStart = command.oldStartEnd[i]; + command.oldStartEnd[i] = oldstartend; + command.seqs[i].setStart(newStart.getBegin()); + command.seqs[i].setEnd(newStart.getEnd()); + } } else { + // decide if we need a new dataset sequence or modify start/end // first edit the original dataset sequence string SequenceI oldds = command.seqs[i].getDatasetSequence(); - String fullseq, osp = oldds.getSequenceAsString(); - - fullseq = osp.substring(0, ipos) + nogaprep - + osp.substring(ipos + nogaprep.length()); + String osp = oldds.getSequenceAsString(); + 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)) @@ -817,13 +838,21 @@ 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); 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. @@ -846,7 +875,8 @@ public class EditCommand implements CommandI { // modification at end command.seqs[i].setEnd( - beforeEditedPositions.getEnd() + nogaprep.length()); + beforeEditedPositions.getEnd() + nogaprep.length() + - nogapold.length()); } else if (afterEditedPositions != null && beforeEditedPositions == null) @@ -860,8 +890,7 @@ 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, + String nogapalseq = AlignSeq.extractGaps(Comparison.GapChars, command.seqs[i].getSequenceAsString().toUpperCase()); int newStart = command.seqs[i].getDatasetSequence() .getSequenceAsString().indexOf(nogapalseq); @@ -891,7 +920,7 @@ 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) { @@ -1049,7 +1078,7 @@ public class EditCommand implements CommandI if (!insert) { - command.deletedAnnotations = new Hashtable(); + command.deletedAnnotations = new Hashtable<>(); } int aSize; @@ -1333,7 +1362,7 @@ public class EditCommand implements CommandI */ public Map priorState(boolean forUndo) { - Map result = new HashMap(); + Map result = new HashMap<>(); if (getEdits() == null) { return result; @@ -1366,7 +1395,7 @@ 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(); @@ -1455,6 +1484,12 @@ public class EditCommand implements CommandI private 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) { @@ -1527,6 +1562,16 @@ public class EditCommand implements CommandI { return gapChar; } + + public void setSystemGenerated(boolean b) + { + systemGenerated = b; + } + + public boolean isSystemGenerated() + { + return systemGenerated; + } } /** @@ -1544,7 +1589,7 @@ public class EditCommand implements CommandI } else { - return new ReverseListIterator(getEdits()); + return new ReverseListIterator<>(getEdits()); } }