X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcommands%2FEditCommand.java;h=aff8595b99cb90981ff9730c7fbb089892e85145;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=a53798ac9ae24c3a8b3c9beb9b480599fcc71bc2;hpb=ebb678af128304dc13e1b6ec9e0961489bf83d39;p=jalview.git
diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index a53798a..aff8595 100644
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -1,285 +1,1103 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
- */
-package jalview.commands;
-
-import jalview.datamodel.*;
-
-/**
- *
- * Title: EditCommmand
- *
- * Description: Essential information for performing
- * undo and redo for cut/paste insert/delete gap
- * which can be stored in the HistoryList
- *
- * Copyright: Copyright (c) 2006
- *
- * Company: Dundee University
- *
- * @author not attributable
- * @version 1.0
- */
-public class EditCommand implements CommandI
-{
- public static String INSERT_GAP = "InsertGap";
- public static String DELETE_GAP = "DeleteGap";
- public static String CUT = "Cut";
- public static String PASTE = "Paste";
-
- Edit[] edits;
-
- String description;
-
- public EditCommand()
- {}
-
- public EditCommand(String description)
- {
- this.description = description;
- }
-
- public EditCommand(String description,
- String command,
- SequenceI[] seqs,
- int position,
- int number,
- char gapChar)
- {
- this.description = description;
-
- if (command.equalsIgnoreCase(INSERT_GAP)
- || command.equalsIgnoreCase(DELETE_GAP))
- {
- edits = new Edit[] { new Edit(command, seqs, position, number, gapChar)};
- }
-
- performEdit(0);
- }
-
- public EditCommand( String description,
- String command,
- SequenceI[] seqs,
- int position,
- int number,
- AlignmentI al)
- {
- this.description = description;
- if ( command.equalsIgnoreCase(CUT) || command.equalsIgnoreCase(PASTE))
- {
- edits = new Edit[]{new Edit(command, seqs, position, number, al)};
- }
-
- performEdit(0);
- }
-
-
- public String getDescription()
- {
- return description;
- }
-
- public int getSize()
- {
- return edits==null?0:edits.length;
- }
-
-
- public void appendEdit(String command,
- SequenceI[] seqs,
- int position,
- int number,
- char gapChar,
- boolean performEdit)
- {
- Edit edit = new Edit(command, seqs, position, number, gapChar);
-
- if (edits != null)
- {
- Edit[] temp = new Edit[edits.length + 1];
- System.arraycopy(edits, 0, temp, 0, edits.length);
- edits = temp;
- edits[edits.length - 1] = edit;
- }
- else
- edits = new Edit[] { edit };
-
- if (performEdit)
- performEdit(edits.length - 1);
- }
-
- void performEdit(int commandIndex)
- {
- int eSize = edits.length;
- for (int e = commandIndex; e < eSize; e++)
- {
- if (edits[e].command.equals(INSERT_GAP))
- {
- insertGap(edits[e]);
- }
- else if (edits[e].command.equals(DELETE_GAP))
- {
- deleteGap(edits[e]);
- }
- else if(edits[e].command.equals(CUT))
- {
- cut(edits[e]);
- }
- else if(edits[e].command.equals(PASTE))
- {
- paste(edits[e]);
- }
- }
- }
-
- public void doCommand()
- {
- performEdit(0);
- }
-
- public void undoCommand()
- {
- int e = 0, eSize = edits.length;
- for (e = eSize-1; e > -1; e--)
- {
- if (edits[e].command.equals(INSERT_GAP))
- {
- deleteGap(edits[e]);
- }
- else if (edits[e].command.equals(DELETE_GAP))
- {
- insertGap(edits[e]);
- }
- else if (edits[e].command.equals(CUT))
- {
- paste(edits[e]);
- }
- else if (edits[e].command.equals(PASTE))
- {
- cut(edits[e]);
- }
- }
- }
-
- void insertGap(Edit command)
- {
- for(int s=0; s.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.commands;
+
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.ListIterator;
+
+/**
+ *
+ *
+ * Title: EditCommmand
+ *
+ *
+ *
+ * Description: Essential information for performing undo and redo for cut/paste
+ * insert/delete gap which can be stored in the HistoryList
+ *
+ *
+ *
+ * Copyright: Copyright (c) 2006
+ *
+ *
+ *
+ * Company: Dundee University
+ *
+ *
+ * @author not attributable
+ * @version 1.0
+ */
+public class EditCommand implements CommandI
+{
+ public enum Action
+ {
+ INSERT_GAP, DELETE_GAP, CUT, PASTE, REPLACE, INSERT_NUC
+ };
+
+ private List edits = new ArrayList();
+
+ String description;
+
+ public EditCommand()
+ {
+ }
+
+ public EditCommand(String description)
+ {
+ this.description = description;
+ }
+
+ public EditCommand(String description, Action command, SequenceI[] seqs,
+ int position, int number, AlignmentI al)
+ {
+ this.description = description;
+ if (command == Action.CUT || command == Action.PASTE)
+ {
+ setEdit(new Edit(command, seqs, position, number, al));
+ }
+
+ performEdit(0, null);
+ }
+
+ public EditCommand(String description, Action command, String replace,
+ SequenceI[] seqs, int position, int number, AlignmentI al)
+ {
+ this.description = description;
+ if (command == Action.REPLACE)
+ {
+ setEdit(new Edit(command, seqs, position, number, al, replace));
+ }
+
+ performEdit(0, null);
+ }
+
+ /**
+ * Set the list of edits to the specified item (only).
+ *
+ * @param e
+ */
+ protected void setEdit(Edit e)
+ {
+ edits.clear();
+ edits.add(e);
+ }
+
+ /**
+ * Add the given edit command to the stored list of commands.
+ *
+ * @param e
+ */
+ protected void addEdit(Edit e)
+ {
+ edits.add(e);
+ }
+
+ /**
+ * Clear the list of stored edit commands.
+ *
+ */
+ protected void clearEdits()
+ {
+ edits.clear();
+ }
+
+ /**
+ * Returns the i'th stored Edit command.
+ *
+ * @param i
+ * @return
+ */
+ protected Edit getEdit(int i)
+ {
+ if (i >= 0 && i < edits.size())
+ {
+ return edits.get(i);
+ }
+ return null;
+ }
+
+ @Override
+ final public String getDescription()
+ {
+ return description;
+ }
+
+ @Override
+ public int getSize()
+ {
+ return edits.size();
+ }
+
+ /**
+ * Return the alignment for the first edit (or null if no edit).
+ *
+ * @return
+ */
+ final public AlignmentI getAlignment()
+ {
+ return (edits.isEmpty() ? null : edits.get(0).al);
+ }
+
+ /**
+ * append a new editCommand Note. this shouldn't be called if the edit is an
+ * operation affects more alignment objects than the one referenced in al (for
+ * example, cut or pasting whole sequences). Use the form with an additional
+ * AlignmentI[] views parameter.
+ *
+ * @param command
+ * @param seqs
+ * @param position
+ * @param number
+ * @param al
+ * @param performEdit
+ */
+ final public void appendEdit(Action command, SequenceI[] seqs,
+ int position,
+ int number, AlignmentI al, boolean performEdit)
+ {
+ appendEdit(command, seqs, position, number, al, performEdit, null);
+ }
+
+ /**
+ * append a new edit command with a set of alignment views that may be
+ * operated on
+ *
+ * @param command
+ * @param seqs
+ * @param position
+ * @param number
+ * @param al
+ * @param performEdit
+ * @param views
+ */
+ final public void appendEdit(Action command, SequenceI[] seqs,
+ int position,
+ int number, AlignmentI al, boolean performEdit, AlignmentI[] views)
+ {
+ Edit edit = new Edit(command, seqs, position, number,
+ al.getGapCharacter());
+ if (al.getHeight() == seqs.length)
+ {
+ edit.al = al;
+ edit.fullAlignmentHeight = true;
+ }
+
+ edits.add(edit);
+
+ if (performEdit)
+ {
+ performEdit(edit, views);
+ }
+ }
+
+ /**
+ * Execute all the edit commands, starting at the given commandIndex
+ *
+ * @param commandIndex
+ * @param views
+ */
+ final void performEdit(int commandIndex, AlignmentI[] views)
+ {
+ ListIterator iterator = edits.listIterator(commandIndex);
+ while (iterator.hasNext())
+ {
+ Edit edit = iterator.next();
+ performEdit(edit, views);
+ }
+ }
+
+ /**
+ * Execute one edit command in all the specified alignment views
+ *
+ * @param edit
+ * @param views
+ */
+ protected void performEdit(Edit edit, AlignmentI[] views)
+ {
+ switch (edit.command)
+ {
+ case INSERT_GAP:
+ insertGap(edit);
+ break;
+ case DELETE_GAP:
+ deleteGap(edit);
+ break;
+ case CUT:
+ cut(edit, views);
+ break;
+ case PASTE:
+ paste(edit, views);
+ break;
+ case REPLACE:
+ replace(edit);
+ break;
+ case INSERT_NUC:
+ // TODO:add deleteNuc for UNDO
+ // case INSERT_NUC:
+ // insertNuc(edits[e]);
+ break;
+ default:
+ break;
+ }
+ }
+
+ @Override
+ final public void doCommand(AlignmentI[] views)
+ {
+ performEdit(0, views);
+ }
+
+ /**
+ * Undo the stored list of commands, in reverse order.
+ */
+ @Override
+ final public void undoCommand(AlignmentI[] views)
+ {
+ ListIterator iterator = edits.listIterator(edits.size());
+ while (iterator.hasPrevious())
+ {
+ Edit e = iterator.previous();
+ switch (e.command)
+ {
+ case INSERT_GAP:
+ deleteGap(e);
+ break;
+ case DELETE_GAP:
+ insertGap(e);
+ break;
+ case CUT:
+ paste(e, views);
+ break;
+ case PASTE:
+ cut(e, views);
+ break;
+ case REPLACE:
+ replace(e);
+ break;
+ case INSERT_NUC:
+ // not implemented
+ break;
+ default:
+ break;
+ }
+ }
+ }
+
+ /**
+ * Insert gap(s) in sequences as specified by the command, and adjust
+ * annotations.
+ *
+ * @param command
+ */
+ final private void insertGap(Edit command)
+ {
+
+ for (int s = 0; s < command.seqs.length; s++)
+ {
+ command.seqs[s].insertCharAt(command.position, command.number,
+ command.gapChar);
+ // System.out.println("pos: "+command.position+" number: "+command.number);
+ }
+
+ adjustAnnotations(command, true, false, null);
+ }
+
+ //
+ // final void insertNuc(Edit command)
+ // {
+ //
+ // for (int s = 0; s < command.seqs.length; s++)
+ // {
+ // System.out.println("pos: "+command.position+" number: "+command.number);
+ // command.seqs[s].insertCharAt(command.position, command.number,'A');
+ // }
+ //
+ // adjustAnnotations(command, true, false, null);
+ // }
+
+ /**
+ * Delete gap(s) in sequences as specified by the command, and adjust
+ * annotations.
+ *
+ * @param command
+ */
+ final private void deleteGap(Edit command)
+ {
+ for (int s = 0; s < command.seqs.length; s++)
+ {
+ command.seqs[s].deleteChars(command.position, command.position
+ + command.number);
+ }
+
+ adjustAnnotations(command, false, false, null);
+ }
+
+ /**
+ * Carry out a Cut action. The cut characters are saved in case Undo is
+ * requested.
+ *
+ * @param command
+ * @param views
+ */
+ void cut(Edit command, AlignmentI[] views)
+ {
+ boolean seqDeleted = false;
+ command.string = new char[command.seqs.length][];
+
+ for (int i = 0; i < command.seqs.length; i++)
+ {
+ final SequenceI sequence = command.seqs[i];
+ if (sequence.getLength() > command.position)
+ {
+ 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);
+ }
+ sequence.deleteChars(command.position, command.position
+ + command.number);
+ if (command.oldds != null && command.oldds[i] != null)
+ {
+ // oldds entry contains the cut dataset sequence.
+ sequence.setDatasetSequence(command.oldds[i]);
+ command.oldds[i] = oldds;
+ }
+ else
+ {
+ // modify the oldds if necessary
+ if (oldds != sequence.getDatasetSequence()
+ || sequence.getSequenceFeatures() != null)
+ {
+ if (command.oldds == null)
+ {
+ command.oldds = new SequenceI[command.seqs.length];
+ }
+ command.oldds[i] = oldds;
+ adjustFeatures(
+ command,
+ i,
+ sequence.findPosition(command.position),
+ sequence.findPosition(command.position
+ + command.number), false);
+ }
+ }
+ }
+
+ if (sequence.getLength() < 1)
+ {
+ command.al.deleteSequence(sequence);
+ seqDeleted = true;
+ }
+ }
+
+ adjustAnnotations(command, false, seqDeleted, views);
+ }
+
+ /**
+ * Perform the given Paste command. This may be to add cut or copied sequences
+ * to an alignment, or to undo a 'Cut' action on a region of the alignment.
+ *
+ * @param command
+ * @param views
+ */
+ 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;
+ if (command.seqs[i].getLength() < 1)
+ {
+ // ie this sequence was deleted, we need to
+ // read it to the alignment
+ if (command.alIndex[i] < command.al.getHeight())
+ {
+ List sequences;
+ synchronized (sequences = command.al.getSequences())
+ {
+ if (!(command.alIndex[i] < 0))
+ {
+ sequences.add(command.alIndex[i], command.seqs[i]);
+ }
+ }
+ }
+ else
+ {
+ command.al.addSequence(command.seqs[i]);
+ }
+ seqWasDeleted = true;
+ }
+ newstart = command.seqs[i].getStart();
+ newend = command.seqs[i].getEnd();
+
+ tmp = new StringBuffer();
+ tmp.append(command.seqs[i].getSequence());
+ // Undo of a delete does not replace original dataset sequence on to
+ // alignment sequence.
+
+ 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)
+ {
+ tmp.append(command.gapChar);
+ length--;
+ }
+ }
+ tmp.insert(command.position, command.string[i]);
+ for (int s = 0; s < command.string[i].length; s++)
+ {
+ if (jalview.schemes.ResidueProperties.aaIndex[command.string[i][s]] != 23)
+ {
+ if (!newDSNeeded)
+ {
+ newDSNeeded = true;
+ start = command.seqs[i].findPosition(command.position);
+ end = command.seqs[i].findPosition(command.position
+ + command.number);
+ }
+ if (command.seqs[i].getStart() == start)
+ {
+ newstart--;
+ }
+ else
+ {
+ newend++;
+ }
+ }
+ }
+ command.string[i] = null;
+ }
+
+ command.seqs[i].setSequence(tmp.toString());
+ command.seqs[i].setStart(newstart);
+ command.seqs[i].setEnd(newend);
+ if (newDSNeeded)
+ {
+ if (command.seqs[i].getDatasetSequence() != null)
+ {
+ SequenceI ds;
+ if (newDSWasNeeded)
+ {
+ ds = command.oldds[i];
+ }
+ else
+ {
+ // make a new DS sequence
+ // use new ds mechanism here
+ ds = new Sequence(command.seqs[i].getName(),
+ jalview.analysis.AlignSeq.extractGaps(
+ jalview.util.Comparison.GapChars,
+ command.seqs[i].getSequenceAsString()),
+ command.seqs[i].getStart(), command.seqs[i].getEnd());
+ ds.setDescription(command.seqs[i].getDescription());
+ }
+ if (command.oldds == null)
+ {
+ command.oldds = new SequenceI[command.seqs.length];
+ }
+ command.oldds[i] = command.seqs[i].getDatasetSequence();
+ command.seqs[i].setDatasetSequence(ds);
+ }
+ adjustFeatures(command, i, start, end, true);
+ }
+ }
+ adjustAnnotations(command, true, seqWasDeleted, views);
+
+ command.string = null;
+ }
+
+ void replace(Edit command)
+ {
+ StringBuffer tmp;
+ String oldstring;
+ int start = command.position;
+ int end = command.number;
+ // TODO TUTORIAL - Fix for replacement with different length of sequence (or
+ // whole sequence)
+ // TODO Jalview 2.4 bugfix change to an aggregate command - original
+ // sequence string is cut, new string is pasted in.
+ command.number = start + command.string[0].length;
+ for (int i = 0; i < command.seqs.length; i++)
+ {
+ boolean newDSWasNeeded = command.oldds != null
+ && command.oldds[i] != null;
+
+ /**
+ * cut addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT,
+ * cut, sg.getStartRes(), sg.getEndRes()-sg.getStartRes()+1,
+ * viewport.alignment));
+ *
+ */
+ /**
+ * then addHistoryItem(new EditCommand( "Add sequences",
+ * EditCommand.PASTE, sequences, 0, alignment.getWidth(), alignment) );
+ *
+ */
+ oldstring = command.seqs[i].getSequenceAsString();
+ 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]));
+ 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]));
+ if (!nogaprep.toLowerCase().equals(nogapold.toLowerCase()))
+ {
+ if (newDSWasNeeded)
+ {
+ SequenceI oldds = command.seqs[i].getDatasetSequence();
+ command.seqs[i].setDatasetSequence(command.oldds[i]);
+ command.oldds[i] = oldds;
+ }
+ else
+ {
+ if (command.oldds == null)
+ {
+ 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);
+
+ }
+ }
+ tmp = null;
+ oldstring = null;
+ }
+ }
+
+ final void adjustAnnotations(Edit command, boolean insert,
+ boolean modifyVisibility, AlignmentI[] views)
+ {
+ AlignmentAnnotation[] annotations = null;
+
+ if (modifyVisibility && !insert)
+ {
+ // only occurs if a sequence was added or deleted.
+ command.deletedAnnotationRows = new Hashtable();
+ }
+ if (command.fullAlignmentHeight)
+ {
+ annotations = command.al.getAlignmentAnnotation();
+ }
+ else
+ {
+ int aSize = 0;
+ AlignmentAnnotation[] tmp;
+ for (int s = 0; s < command.seqs.length; s++)
+ {
+ if (modifyVisibility)
+ {
+ // Rows are only removed or added to sequence object.
+ if (!insert)
+ {
+ // remove rows
+ tmp = command.seqs[s].getAnnotation();
+ if (tmp != null)
+ {
+ int alen = tmp.length;
+ for (int aa = 0; aa < tmp.length; aa++)
+ {
+ if (!command.al.deleteAnnotation(tmp[aa]))
+ {
+ // strip out annotation not in the current al (will be put
+ // back on insert in all views)
+ tmp[aa] = null;
+ alen--;
+ }
+ }
+ command.seqs[s].setAlignmentAnnotation(null);
+ if (alen != tmp.length)
+ {
+ // save the non-null annotation references only
+ AlignmentAnnotation[] saved = new AlignmentAnnotation[alen];
+ for (int aa = 0, aapos = 0; aa < tmp.length; aa++)
+ {
+ if (tmp[aa] != null)
+ {
+ saved[aapos++] = tmp[aa];
+ tmp[aa] = null;
+ }
+ }
+ 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++)
+ {
+ if (views[alview] != command.al)
+ {
+ AlignmentAnnotation[] toremove = views[alview]
+ .getAlignmentAnnotation();
+ if (toremove == null || toremove.length == 0)
+ {
+ continue;
+ }
+ // remove any alignment annotation on this sequence that's
+ // on that alignment view.
+ for (int aa = 0; aa < toremove.length; aa++)
+ {
+ if (toremove[aa].sequenceRef == command.seqs[s])
+ {
+ views[alview].deleteAnnotation(toremove[aa]);
+ }
+ }
+ }
+ }
+ }
+ else
+ {
+ // save all the annotation
+ command.deletedAnnotationRows.put(command.seqs[s], tmp);
+ }
+ }
+ }
+ else
+ {
+ // recover rows
+ if (command.deletedAnnotationRows != null
+ && command.deletedAnnotationRows
+ .containsKey(command.seqs[s]))
+ {
+ AlignmentAnnotation[] revealed = command.deletedAnnotationRows
+ .get(command.seqs[s]);
+ command.seqs[s].setAlignmentAnnotation(revealed);
+ if (revealed != null)
+ {
+ for (int aa = 0; aa < revealed.length; aa++)
+ {
+ // iterate through al adding original annotation
+ command.al.addAnnotation(revealed[aa]);
+ }
+ for (int aa = 0; aa < revealed.length; aa++)
+ {
+ command.al.setAnnotationIndex(revealed[aa], aa);
+ }
+ // and then duplicate added annotation on every other alignment
+ // view
+ for (int vnum = 0; views != null && vnum < views.length; vnum++)
+ {
+ if (views[vnum] != command.al)
+ {
+ int avwidth = views[vnum].getWidth() + 1;
+ // duplicate in this view
+ for (int a = 0; a < revealed.length; a++)
+ {
+ AlignmentAnnotation newann = new AlignmentAnnotation(
+ revealed[a]);
+ command.seqs[s].addAlignmentAnnotation(newann);
+ newann.padAnnotation(avwidth);
+ views[vnum].addAnnotation(newann);
+ views[vnum].setAnnotationIndex(newann, a);
+ }
+ }
+ }
+ }
+ }
+ }
+ continue;
+ }
+
+ if (command.seqs[s].getAnnotation() == null)
+ {
+ continue;
+ }
+
+ if (aSize == 0)
+ {
+ annotations = command.seqs[s].getAnnotation();
+ }
+ else
+ {
+ tmp = new AlignmentAnnotation[aSize
+ + command.seqs[s].getAnnotation().length];
+
+ System.arraycopy(annotations, 0, tmp, 0, aSize);
+
+ System.arraycopy(command.seqs[s].getAnnotation(), 0, tmp, aSize,
+ command.seqs[s].getAnnotation().length);
+
+ annotations = tmp;
+ }
+ aSize = annotations.length;
+ }
+ }
+
+ if (annotations == null)
+ {
+ return;
+ }
+
+ if (!insert)
+ {
+ command.deletedAnnotations = new Hashtable();
+ }
+
+ int aSize;
+ Annotation[] temp;
+ for (int a = 0; a < annotations.length; a++)
+ {
+ if (annotations[a].autoCalculated
+ || annotations[a].annotations == null)
+ {
+ continue;
+ }
+
+ int tSize = 0;
+
+ aSize = annotations[a].annotations.length;
+ if (insert)
+ {
+ temp = new Annotation[aSize + command.number];
+ if (annotations[a].padGaps)
+ {
+ for (int aa = 0; aa < temp.length; aa++)
+ {
+ temp[aa] = new Annotation(command.gapChar + "", null, ' ', 0);
+ }
+ }
+ }
+ else
+ {
+ if (command.position < aSize)
+ {
+ if (command.position + command.number >= aSize)
+ {
+ tSize = aSize;
+ }
+ else
+ {
+ tSize = aSize - command.number;
+ }
+ }
+ else
+ {
+ tSize = aSize;
+ }
+
+ if (tSize < 0)
+ {
+ tSize = aSize;
+ }
+ temp = new Annotation[tSize];
+ }
+
+ if (insert)
+ {
+ if (command.position < annotations[a].annotations.length)
+ {
+ System.arraycopy(annotations[a].annotations, 0, temp, 0,
+ command.position);
+
+ if (command.deletedAnnotations != null
+ && command.deletedAnnotations
+ .containsKey(annotations[a].annotationId))
+ {
+ Annotation[] restore = command.deletedAnnotations
+ .get(annotations[a].annotationId);
+
+ System.arraycopy(restore, 0, temp, command.position,
+ command.number);
+
+ }
+
+ System.arraycopy(annotations[a].annotations, command.position,
+ temp, command.position + command.number, aSize
+ - command.position);
+ }
+ else
+ {
+ if (command.deletedAnnotations != null
+ && command.deletedAnnotations
+ .containsKey(annotations[a].annotationId))
+ {
+ Annotation[] restore = command.deletedAnnotations
+ .get(annotations[a].annotationId);
+
+ temp = new Annotation[annotations[a].annotations.length
+ + restore.length];
+ System.arraycopy(annotations[a].annotations, 0, temp, 0,
+ annotations[a].annotations.length);
+ System.arraycopy(restore, 0, temp,
+ annotations[a].annotations.length, restore.length);
+ }
+ else
+ {
+ temp = annotations[a].annotations;
+ }
+ }
+ }
+ else
+ {
+ if (tSize != aSize || command.position < 2)
+ {
+ int copylen = Math.min(command.position,
+ annotations[a].annotations.length);
+ if (copylen > 0)
+ {
+ System.arraycopy(annotations[a].annotations, 0, temp, 0,
+ copylen); // command.position);
+ }
+
+ Annotation[] deleted = new Annotation[command.number];
+ if (copylen >= command.position)
+ {
+ copylen = Math.min(command.number,
+ annotations[a].annotations.length - command.position);
+ if (copylen > 0)
+ {
+ System.arraycopy(annotations[a].annotations,
+ command.position, deleted, 0, copylen); // command.number);
+ }
+ }
+
+ command.deletedAnnotations.put(annotations[a].annotationId,
+ deleted);
+ 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
+ }
+ }
+ else
+ {
+ int dSize = aSize - command.position;
+
+ if (dSize > 0)
+ {
+ Annotation[] deleted = new Annotation[command.number];
+ System.arraycopy(annotations[a].annotations, command.position,
+ deleted, 0, dSize);
+
+ command.deletedAnnotations.put(annotations[a].annotationId,
+ deleted);
+
+ tSize = Math.min(annotations[a].annotations.length,
+ command.position);
+ temp = new Annotation[tSize];
+ System.arraycopy(annotations[a].annotations, 0, temp, 0, tSize);
+ }
+ else
+ {
+ temp = annotations[a].annotations;
+ }
+ }
+ }
+
+ annotations[a].annotations = temp;
+ }
+ }
+
+ final void adjustFeatures(Edit command, int index, int i, int j,
+ boolean insert)
+ {
+ SequenceI seq = command.seqs[index];
+ SequenceI sequence = seq.getDatasetSequence();
+ if (sequence == null)
+ {
+ sequence = seq;
+ }
+
+ if (insert)
+ {
+ if (command.editedFeatures != null
+ && command.editedFeatures.containsKey(seq))
+ {
+ sequence.setSequenceFeatures(command.editedFeatures
+ .get(seq));
+ }
+
+ return;
+ }
+
+ SequenceFeature[] sf = sequence.getSequenceFeatures();
+
+ if (sf == null)
+ {
+ return;
+ }
+
+ SequenceFeature[] oldsf = new SequenceFeature[sf.length];
+
+ int cSize = j - i;
+
+ for (int s = 0; s < sf.length; s++)
+ {
+ SequenceFeature copy = new SequenceFeature(sf[s]);
+
+ oldsf[s] = copy;
+
+ if (sf[s].getEnd() < i)
+ {
+ continue;
+ }
+
+ if (sf[s].getBegin() > j)
+ {
+ sf[s].setBegin(copy.getBegin() - cSize);
+ sf[s].setEnd(copy.getEnd() - cSize);
+ continue;
+ }
+
+ if (sf[s].getBegin() >= i)
+ {
+ sf[s].setBegin(i);
+ }
+
+ if (sf[s].getEnd() < j)
+ {
+ sf[s].setEnd(j - 1);
+ }
+
+ sf[s].setEnd(sf[s].getEnd() - (cSize));
+
+ if (sf[s].getBegin() > sf[s].getEnd())
+ {
+ sequence.deleteFeature(sf[s]);
+ }
+ }
+
+ if (command.editedFeatures == null)
+ {
+ command.editedFeatures = new Hashtable();
+ }
+
+ command.editedFeatures.put(seq, oldsf);
+
+ }
+
+ class Edit
+ {
+ public SequenceI[] oldds;
+
+ boolean fullAlignmentHeight = false;
+
+ Hashtable deletedAnnotationRows;
+
+ Hashtable deletedAnnotations;
+
+ Hashtable editedFeatures;
+
+ AlignmentI al;
+
+ Action command;
+
+ char[][] string;
+
+ SequenceI[] seqs;
+
+ int[] alIndex;
+
+ int position, number;
+
+ char gapChar;
+
+ Edit(Action command, SequenceI[] seqs, int position, int number,
+ char gapChar)
+ {
+ this.command = command;
+ this.seqs = seqs;
+ this.position = position;
+ this.number = number;
+ this.gapChar = gapChar;
+ }
+
+ Edit(Action command, SequenceI[] seqs, int position, int number,
+ AlignmentI al)
+ {
+ 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++)
+ {
+ alIndex[i] = al.findIndex(seqs[i]);
+ }
+
+ fullAlignmentHeight = (al.getHeight() == seqs.length);
+ }
+
+ Edit(Action command, SequenceI[] seqs, int position, int number,
+ AlignmentI al, 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++)
+ {
+ string[i] = replace.toCharArray();
+ }
+
+ fullAlignmentHeight = (al.getHeight() == seqs.length);
+ }
+ }
+}