X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcommands%2FEditCommand.java;h=cac843f8488e9877ae5abbdd535e90a497b22fb6;hb=refs%2Fheads%2Fportforward%2FJAL-2675_2102b1to2103;hp=7a049493f6b5f5a6596553ed6249948f302354b1;hpb=1e085f14ae2f19adfac0153c437ee891f0ad07bc;p=jalview.git diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java index 7a04949..cac843f 100644 --- a/src/jalview/commands/EditCommand.java +++ b/src/jalview/commands/EditCommand.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) - * Copyright (C) 2015 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -122,15 +122,15 @@ public class EditCommand implements CommandI { } - public EditCommand(String description) + public EditCommand(String desc) { - this.description = description; + this.description = desc; } - public EditCommand(String description, Action command, SequenceI[] seqs, + public EditCommand(String desc, Action command, SequenceI[] seqs, int position, int number, AlignmentI al) { - this.description = description; + this.description = desc; if (command == Action.CUT || command == Action.PASTE) { setEdit(new Edit(command, seqs, position, number, al)); @@ -139,10 +139,10 @@ public class EditCommand implements CommandI performEdit(0, null); } - public EditCommand(String description, Action command, String replace, + public EditCommand(String desc, Action command, String replace, SequenceI[] seqs, int position, int number, AlignmentI al) { - this.description = description; + this.description = desc; if (command == Action.REPLACE) { setEdit(new Edit(command, seqs, position, number, al, replace)); @@ -222,14 +222,16 @@ public class EditCommand implements CommandI /** * Check a contiguous edit; either * */ - boolean contiguous = (action == Action.INSERT_GAP && e.position == lastEdit.position - + lastEdit.number) - || (action == Action.DELETE_GAP && e.position + e.number == lastEdit.position); + boolean contiguous = (action == Action.INSERT_GAP + && e.position == lastEdit.position + lastEdit.number) + || (action == Action.DELETE_GAP + && e.position + e.number == lastEdit.position); if (contiguous) { /* @@ -475,7 +477,8 @@ public class EditCommand implements CommandI { command.seqs[s].insertCharAt(command.position, command.number, command.gapChar); - // System.out.println("pos: "+command.position+" number: "+command.number); + // System.out.println("pos: "+command.position+" number: + // "+command.number); } adjustAnnotations(command, true, false, null); @@ -504,8 +507,8 @@ public class EditCommand implements CommandI { for (int s = 0; s < command.seqs.length; s++) { - command.seqs[s].deleteChars(command.position, command.position - + command.number); + command.seqs[s].deleteChars(command.position, + command.position + command.number); } adjustAnnotations(command, false, false, null); @@ -536,8 +539,8 @@ public class EditCommand implements CommandI // we are redoing an undone cut. sequence.setDatasetSequence(null); } - sequence.deleteChars(command.position, command.position - + command.number); + sequence.deleteChars(command.position, + command.position + command.number); if (command.oldds != null && command.oldds[i] != null) { // oldds entry contains the cut dataset sequence. @@ -548,13 +551,14 @@ public class EditCommand implements CommandI { // modify the oldds if necessary if (oldds != sequence.getDatasetSequence() - || sequence.getSequenceFeatures() != null) + || sequence.getFeatures().hasFeatures()) { if (command.oldds == null) { command.oldds = new SequenceI[command.seqs.length]; } command.oldds[i] = oldds; + // FIXME JAL-2541 JAL-2526 get correct positions if on a gap adjustFeatures( command, i, @@ -646,8 +650,8 @@ public class EditCommand implements CommandI { newDSNeeded = true; start = command.seqs[i].findPosition(command.position); - end = command.seqs[i].findPosition(command.position - + command.number); + end = command.seqs[i] + .findPosition(command.position + command.number); } if (command.seqs[i].getStart() == start) { @@ -731,16 +735,16 @@ public class EditCommand implements CommandI tmp = new StringBuffer(oldstring.substring(0, start)); tmp.append(command.string[i]); String nogaprep = jalview.analysis.AlignSeq.extractGaps( - jalview.util.Comparison.GapChars, new String( - command.string[i])); + jalview.util.Comparison.GapChars, + new String(command.string[i])); int ipos = command.seqs[i].findPosition(start) - command.seqs[i].getStart(); tmp.append(oldstring.substring(end)); command.seqs[i].setSequence(tmp.toString()); command.string[i] = oldstring.substring(start, end).toCharArray(); String nogapold = jalview.analysis.AlignSeq.extractGaps( - jalview.util.Comparison.GapChars, new String( - command.string[i])); + jalview.util.Comparison.GapChars, + new String(command.string[i])); if (!nogaprep.toLowerCase().equals(nogapold.toLowerCase())) { if (newDSWasNeeded) @@ -797,6 +801,8 @@ public class EditCommand implements CommandI AlignmentAnnotation[] tmp; for (int s = 0; s < command.seqs.length; s++) { + command.seqs[s].sequenceChanged(); + if (modifyVisibility) { // Rows are only removed or added to sequence object. @@ -833,7 +839,8 @@ public class EditCommand implements CommandI tmp = saved; command.deletedAnnotationRows.put(command.seqs[s], saved); // and then remove any annotation in the other views - for (int alview = 0; views != null && alview < views.length; alview++) + for (int alview = 0; views != null + && alview < views.length; alview++) { if (views[alview] != command.al) { @@ -885,7 +892,8 @@ 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) { @@ -1012,8 +1020,8 @@ public class EditCommand implements CommandI } System.arraycopy(annotations[a].annotations, command.position, - temp, command.position + command.number, aSize - - command.position); + temp, command.position + command.number, + aSize - command.position); } else { @@ -1056,8 +1064,8 @@ public class EditCommand implements CommandI annotations[a].annotations.length - command.position); if (copylen > 0) { - System.arraycopy(annotations[a].annotations, - command.position, deleted, 0, copylen); // command.number); + System.arraycopy(annotations[a].annotations, command.position, + deleted, 0, copylen); // command.number); } } @@ -1066,10 +1074,10 @@ public class EditCommand implements CommandI if (annotations[a].annotations.length > command.position + command.number) { - System.arraycopy(annotations[a].annotations, command.position - + command.number, temp, command.position, - annotations[a].annotations.length - command.position - - command.number); // aSize + System.arraycopy(annotations[a].annotations, + command.position + command.number, temp, + command.position, annotations[a].annotations.length + - command.position - command.number); // aSize } } else @@ -1101,8 +1109,8 @@ public class EditCommand implements CommandI } } - final static void adjustFeatures(Edit command, int index, int i, int j, - boolean insert) + final static void adjustFeatures(Edit command, int index, final int i, + final int j, boolean insert) { SequenceI seq = command.seqs[index]; SequenceI sequence = seq.getDatasetSequence(); @@ -1122,56 +1130,73 @@ public class EditCommand implements CommandI return; } - SequenceFeature[] sf = sequence.getSequenceFeatures(); + List sf = sequence.getFeatures() + .getPositionalFeatures(); - if (sf == null) + if (sf.isEmpty()) { return; } - SequenceFeature[] oldsf = new SequenceFeature[sf.length]; + List oldsf = new ArrayList(); int cSize = j - i; - for (int s = 0; s < sf.length; s++) + for (SequenceFeature feature : sf) { - SequenceFeature copy = new SequenceFeature(sf[s]); + SequenceFeature copy = new SequenceFeature(feature); - oldsf[s] = copy; + oldsf.add(copy); - if (sf[s].getEnd() < i) + if (feature.getEnd() < i) { continue; } - if (sf[s].getBegin() > j) + if (feature.getBegin() > j) { - sf[s].setBegin(copy.getBegin() - cSize); - sf[s].setEnd(copy.getEnd() - cSize); + int newBegin = copy.getBegin() - cSize; + int newEnd = copy.getEnd() - cSize; + SequenceFeature newSf = new SequenceFeature(feature, newBegin, + newEnd, feature.getFeatureGroup(), feature.getScore()); + sequence.deleteFeature(feature); + sequence.addSequenceFeature(newSf); + // feature.setBegin(newBegin); + // feature.setEnd(newEnd); continue; } - if (sf[s].getBegin() >= i) + int newBegin = feature.getBegin(); + int newEnd = feature.getEnd(); + if (newBegin >= i) { - sf[s].setBegin(i); + newBegin = i; + // feature.setBegin(i); } - if (sf[s].getEnd() < j) + if (newEnd < j) { - sf[s].setEnd(j - 1); + newEnd = j - 1; + // feature.setEnd(j - 1); } + newEnd = newEnd - cSize; + // feature.setEnd(feature.getEnd() - (cSize)); - sf[s].setEnd(sf[s].getEnd() - (cSize)); - - if (sf[s].getBegin() > sf[s].getEnd()) + sequence.deleteFeature(feature); + if (newEnd >= newBegin) { - sequence.deleteFeature(sf[s]); + sequence.addSequenceFeature(new SequenceFeature(feature, newBegin, + newEnd, feature.getFeatureGroup(), feature.getScore())); } + // if (feature.getBegin() > feature.getEnd()) + // { + // sequence.deleteFeature(feature); + // } } if (command.editedFeatures == null) { - command.editedFeatures = new Hashtable(); + command.editedFeatures = new Hashtable>(); } command.editedFeatures.put(seq, oldsf); @@ -1298,7 +1323,7 @@ public class EditCommand implements CommandI Hashtable deletedAnnotations; - Hashtable editedFeatures; + Hashtable> editedFeatures; AlignmentI al; @@ -1314,51 +1339,51 @@ public class EditCommand implements CommandI char gapChar; - public Edit(Action command, SequenceI[] seqs, int position, int number, - char gapChar) + public Edit(Action cmd, SequenceI[] sqs, int pos, int count, + char gap) { - this.command = command; - this.seqs = seqs; - this.position = position; - this.number = number; - this.gapChar = gapChar; + this.command = cmd; + this.seqs = sqs; + this.position = pos; + this.number = count; + this.gapChar = gap; } - Edit(Action command, SequenceI[] seqs, int position, int number, - AlignmentI al) + Edit(Action cmd, SequenceI[] sqs, int pos, int count, + AlignmentI align) { - this.gapChar = al.getGapCharacter(); - this.command = command; - this.seqs = seqs; - this.position = position; - this.number = number; - this.al = al; - - alIndex = new int[seqs.length]; - for (int i = 0; i < seqs.length; i++) + this.gapChar = align.getGapCharacter(); + this.command = cmd; + this.seqs = sqs; + this.position = pos; + this.number = count; + this.al = align; + + alIndex = new int[sqs.length]; + for (int i = 0; i < sqs.length; i++) { - alIndex[i] = al.findIndex(seqs[i]); + alIndex[i] = align.findIndex(sqs[i]); } - fullAlignmentHeight = (al.getHeight() == seqs.length); + fullAlignmentHeight = (align.getHeight() == sqs.length); } - Edit(Action command, SequenceI[] seqs, int position, int number, - AlignmentI al, String replace) + Edit(Action cmd, SequenceI[] sqs, int pos, int count, + AlignmentI align, String replace) { - this.command = command; - this.seqs = seqs; - this.position = position; - this.number = number; - this.al = al; - this.gapChar = al.getGapCharacter(); - string = new char[seqs.length][]; - for (int i = 0; i < seqs.length; i++) + this.command = cmd; + this.seqs = sqs; + this.position = pos; + this.number = count; + this.al = align; + this.gapChar = align.getGapCharacter(); + string = new char[sqs.length][]; + for (int i = 0; i < sqs.length; i++) { string[i] = replace.toCharArray(); } - fullAlignmentHeight = (al.getHeight() == seqs.length); + fullAlignmentHeight = (align.getHeight() == sqs.length); } public SequenceI[] getSequences()