X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcommands%2FEditCommand.java;h=30595bce2afcec658ce343e5ee7067bcd3310c03;hb=9d2408483e451285fd555c3cd6e0273977acbaa7;hp=53c2628829a48373a3c24047b6d165c60c2c2788;hpb=35e4bf27849cd0c5250749cca6d22bfc23b6d360;p=jalview.git diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java index 53c2628..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; @@ -526,37 +529,48 @@ 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(); + + /* + * perform the cut; if this results in a new dataset sequence, add + * that to the alignment dataset + */ + SequenceI ds = sequence.getDatasetSequence(); sequence.deleteChars(command.position, command.position + command.number); if (command.oldds != null && command.oldds[i] != null) { - // oldds entry contains the cut dataset sequence. + /* + * 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 { - // modify the oldds if necessary - if (oldds != sequence.getDatasetSequence() - || sequence.getFeatures().hasFeatures()) + /* + * new cut operation: save the dataset sequence + * so it can be restored in an Undo + */ + if (command.oldds == null) { - if (command.oldds == null) - { - command.oldds = new SequenceI[command.seqs.length]; - } - command.oldds[i] = oldds; + command.oldds = new SequenceI[command.seqs.length]; + } + command.oldds[i] = oldds;// todo not if !cutIsInternal? + // do we need to edit sequence features for new sequence ? + if (oldds != sequence.getDatasetSequence() + || (cutIsInternal + && sequence.getFeatures().hasFeatures())) + // todo or just test cutIsInternal && cutPositions != null ? + { if (cutPositions != null) { cutFeatures(command, sequence, cutPositions.getBegin(), @@ -564,6 +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) @@ -585,26 +606,23 @@ public class EditCommand implements CommandI */ static void paste(Edit command, AlignmentI[] views) { - StringBuffer tmp; - boolean newDSNeeded; - boolean newDSWasNeeded; - int newstart, newend; boolean seqWasDeleted = false; - int start = 0, end = 0; for (int i = 0; i < command.seqs.length; i++) { - newDSNeeded = false; - newDSWasNeeded = command.oldds != null && command.oldds[i] != null; + boolean newDSNeeded = false; + boolean newDSWasNeeded = command.oldds != null + && command.oldds[i] != null; SequenceI sequence = command.seqs[i]; if (sequence.getLength() < 1) { - // ie this sequence was deleted, we need to - // readd it to the alignment + /* + * sequence was deleted; re-add it to the alignment + */ 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)) { @@ -618,25 +636,28 @@ public class EditCommand implements CommandI } seqWasDeleted = true; } - newstart = sequence.getStart(); - newend = sequence.getEnd(); + int newStart = sequence.getStart(); + int newEnd = sequence.getEnd(); - tmp = new StringBuffer(); + StringBuilder tmp = new StringBuilder(); tmp.append(sequence.getSequence()); // Undo of a delete does not replace original dataset sequence on to // alignment sequence. + int start = 0; + int length = 0; + if (command.string != null && command.string[i] != null) { if (command.position >= tmp.length()) { // This occurs if padding is on, and residues // are removed from end of alignment - int length = command.position - tmp.length(); - while (length > 0) + int len = command.position - tmp.length(); + while (len > 0) { tmp.append(command.gapChar); - length--; + len--; } } tmp.insert(command.position, command.string[i]); @@ -644,20 +665,21 @@ public class EditCommand implements CommandI { if (!Comparison.isGap(command.string[i][s])) { + length++; if (!newDSNeeded) { newDSNeeded = true; start = sequence.findPosition(command.position); - end = sequence.findPosition(command.position - + command.number); + // end = sequence + // .findPosition(command.position + command.number); } if (sequence.getStart() == start) { - newstart--; + newStart--; } else { - newend++; + newEnd++; } } } @@ -665,8 +687,14 @@ public class EditCommand implements CommandI } sequence.setSequence(tmp.toString()); - sequence.setStart(newstart); - sequence.setEnd(newend); + sequence.setStart(newStart); + sequence.setEnd(newEnd); + + /* + * command and Undo share the same dataset sequence if cut was + * at start or end of sequence + */ + boolean sameDatasetSequence = false; if (newDSNeeded) { if (sequence.getDatasetSequence() != null) @@ -691,9 +719,18 @@ public class EditCommand implements CommandI command.oldds = new SequenceI[command.seqs.length]; } 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, i, start, end); + undoCutFeatures(command, command.seqs[i], start, length, + sameDatasetSequence); } } adjustAnnotations(command, true, seqWasDeleted, views); @@ -703,7 +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; @@ -716,6 +753,7 @@ public class EditCommand implements CommandI { boolean newDSWasNeeded = command.oldds != null && command.oldds[i] != null; + boolean newStartEndWasNeeded = command.oldStartEnd!=null && command.oldStartEnd[i]!=null; /** * cut addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, @@ -728,49 +766,147 @@ public class EditCommand implements CommandI * EditCommand.PASTE, sequences, 0, alignment.getWidth(), alignment) ); * */ + 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(); - tmp.append(oldstring.substring(end)); + 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, end).toCharArray(); - String nogapold = jalview.analysis.AlignSeq.extractGaps( - jalview.util.Comparison.GapChars, + command.string[i] = oldstring + .substring(start, Math.min(end, oldstring.length())) + .toCharArray(); + 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))) { - 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; + } + if (newStartEndWasNeeded) + { + Range newStart = command.oldStartEnd[i]; + command.oldStartEnd[i] = oldstartend; + command.seqs[i].setStart(newStart.getBegin()); + command.seqs[i].setEnd(newStart.getEnd()); + } } - else + else { - if (command.oldds == null) + // 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 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)) { - command.oldds = new SequenceI[command.seqs.length]; - } - command.oldds[i] = command.seqs[i].getDatasetSequence(); - SequenceI newds = new Sequence( - command.seqs[i].getDatasetSequence()); - String fullseq, osp = newds.getSequenceAsString(); - fullseq = osp.substring(0, ipos) + nogaprep - + osp.substring(ipos + nogaprep.length()); - newds.setSequence(fullseq.toUpperCase()); - // TODO: JAL-1131 ensure newly created dataset sequence is added to - // the set of - // dataset sequences associated with the alignment. - // TODO: JAL-1131 fix up any annotation associated with new dataset - // sequence to ensure that original sequence/annotation relationships - // are preserved. - command.seqs[i].setDatasetSequence(newds); + // old ds and edited ds are different, so + // create the new dataset sequence + SequenceI newds = new Sequence(oldds); + 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. + // TODO: JAL-1131 fix up any annotation associated with new dataset + // sequence to ensure that original sequence/annotation + // relationships + // are preserved. + command.seqs[i].setDatasetSequence(newds); + } + else + { + if (command.oldStartEnd == null) + { + command.oldStartEnd = new Range[command.seqs.length]; + } + command.oldStartEnd[i] = new Range(command.seqs[i].getStart(), + command.seqs[i].getEnd()); + if (beforeEditedPositions != null + && afterEditedPositions == null) + { + // modification at end + command.seqs[i].setEnd( + beforeEditedPositions.getEnd() + nogaprep.length() + - nogapold.length()); + } + else if (afterEditedPositions != null + && beforeEditedPositions == null) + { + // modification at start + command.seqs[i].setStart( + afterEditedPositions.getBegin() - nogaprep.length()); + } + else + { + // edit covered both start and end. Here we can only guess the + // new + // start/end + 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) + { + throw new Error( + "Implementation Error: could not locate start/end " + + "in dataset sequence after an edit of the sequence string"); + } + int newEnd = newStart + nogapalseq.length() - 1; + command.seqs[i].setStart(newStart); + command.seqs[i].setEnd(newEnd); + } + } } } tmp = null; @@ -786,7 +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) { @@ -889,8 +1025,7 @@ public class EditCommand implements CommandI } // and then duplicate added annotation on every other alignment // view - for (int vnum = 0; views != null - && vnum < views.length; vnum++) + for (int vnum = 0; views != null && vnum < views.length; vnum++) { if (views[vnum] != command.al) { @@ -945,7 +1080,7 @@ public class EditCommand implements CommandI if (!insert) { - command.deletedAnnotations = new Hashtable(); + command.deletedAnnotations = new Hashtable<>(); } int aSize; @@ -1106,10 +1241,29 @@ public class EditCommand implements CommandI } } - final static void undoCutFeatures(Edit command, int index, final int i, - final int j) + /** + * Restores features to the state before a Cut. + *
    + *
  • re-add any features deleted by the cut
    • + *
  • remove any truncated features created by the cut
    • + *
  • shift right any features to the right of the cut
    • + *
+ * + * @param command + * the Cut command + * @param seq + * the sequence the Cut applied to + * @param start + * the start residue position of the cut + * @param length + * the number of residues cut + * @param sameDatasetSequence + * true if dataset sequence and frame of reference were left + * unchanged by the Cut + */ + final static void undoCutFeatures(Edit command, SequenceI seq, + final int start, final int length, boolean sameDatasetSequence) { - SequenceI seq = command.seqs[index]; SequenceI sequence = seq.getDatasetSequence(); if (sequence == null) { @@ -1117,10 +1271,43 @@ public class EditCommand implements CommandI } /* - * TODO: shift right features that lie to the right of the restored cut - * Currently not needed as all features restored with saved dataset sequence - * nor if no saved dataset sequence (as coordinates left unchanged by Cut) + * shift right features that lie to the right of the restored cut (but not + * if dataset sequence unchanged - so coordinates were changed by Cut) */ + if (!sameDatasetSequence) + { + /* + * shift right all features right of and not + * contiguous with the cut position + */ + seq.getFeatures().shiftFeatures(start + 1, length); + + /* + * shift right any features that start at the cut position, + * unless they were truncated + */ + List sfs = seq.getFeatures().findFeatures(start, + start); + for (SequenceFeature sf : sfs) + { + if (sf.getBegin() == start) + { + if (!command.truncatedFeatures.containsKey(seq) + || !command.truncatedFeatures.get(seq).contains(sf)) + { + /* + * feature was shifted left to cut position (not truncated), + * so shift it back right + */ + SequenceFeature shifted = new SequenceFeature(sf, sf.getBegin() + + length, sf.getEnd() + length, sf.getFeatureGroup(), + sf.getScore()); + seq.addSequenceFeature(shifted); + seq.deleteFeature(sf); + } + } + } + } /* * restore any features that were deleted or truncated @@ -1177,7 +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; @@ -1210,7 +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(); @@ -1259,7 +1446,12 @@ public class EditCommand implements CommandI public class Edit { - public SequenceI[] oldds; + SequenceI[] oldds; + + /** + * start and end of sequence prior to edit + */ + Range[] oldStartEnd; boolean fullAlignmentHeight = false; @@ -1280,7 +1472,7 @@ public class EditCommand implements CommandI AlignmentI al; - Action command; + final Action command; char[][] string; @@ -1288,10 +1480,18 @@ public class EditCommand implements CommandI int[] alIndex; - int position, number; + int position; + + int number; 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) { @@ -1318,6 +1518,16 @@ public class EditCommand implements CommandI fullAlignmentHeight = (align.getHeight() == sqs.length); } + /** + * Constructor given a REPLACE command and the replacement string + * + * @param cmd + * @param sqs + * @param pos + * @param count + * @param align + * @param replace + */ Edit(Action cmd, SequenceI[] sqs, int pos, int count, AlignmentI align, String replace) { @@ -1354,6 +1564,16 @@ public class EditCommand implements CommandI { return gapChar; } + + public void setSystemGenerated(boolean b) + { + systemGenerated = b; + } + + public boolean isSystemGenerated() + { + return systemGenerated; + } } /** @@ -1371,7 +1591,7 @@ public class EditCommand implements CommandI } else { - return new ReverseListIterator(getEdits()); + return new ReverseListIterator<>(getEdits()); } } @@ -1382,7 +1602,7 @@ public class EditCommand implements CommandI *
  • features right of the cut are shifted left
    • *
  • features internal to the cut region are deleted
    • *
  • features that overlap or span the cut are shortened
    • - *
  • the originals of any deleted or shorted features are saved, to re-add + *
  • the originals of any deleted or shortened features are saved, to re-add * on Undo
    • *
  • any added (shortened) features are saved, to delete on Undo
    • * @@ -1396,6 +1616,14 @@ public class EditCommand implements CommandI protected static void cutFeatures(Edit command, SequenceI seq, int fromPosition, int toPosition, boolean cutIsInternal) { + /* + * if the cut is at start or end of sequence + * then we don't modify the sequence feature store + */ + if (!cutIsInternal) + { + return; + } List added = new ArrayList<>(); List removed = new ArrayList<>(); @@ -1418,6 +1646,19 @@ public class EditCommand implements CommandI cutStartPos, cutEndPos); /* + * add any contact features that span the cut region + * (not returned by findFeatures) + */ + for (SequenceFeature contact : featureStore.getContactFeatures()) + { + if (contact.getBegin() < cutStartPos + && contact.getEnd() > cutEndPos) + { + toAmend.add(contact); + } + } + + /* * adjust start-end of overlapping features; * delete features enclosed by the cut; * delete partially overlapping contact features @@ -1463,7 +1704,6 @@ public class EditCommand implements CommandI * truncate left, adjust end of feature */ newBegin = cutIsInternal ? cutStartPos : cutEndPos + 1; - // newEnd = newBegin + (sfEnd - sfBegin) - overlapsBy; newEnd = newBegin + sfEnd - cutEndPos - 1; if (sf.isContactFeature()) { @@ -1490,12 +1730,9 @@ public class EditCommand implements CommandI /* * and left shift any features lying to the right of the cut region - * (but not if the cut is at start or end of sequence) */ - if (cutIsInternal) - { - featureStore.shiftFeatures(cutEndPos + 1, -cutWidth); - } + + featureStore.shiftFeatures(cutEndPos + 1, -cutWidth); } /*