X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcommands%2FEditCommand.java;h=b39d1ddb69302035d183b18778a8c6939ee39b46;hb=9157d82cb9213d9071c15203dddf96ae9081dfbe;hp=03b94d3ca6dcfe7921526636ea6f90fad7b353c5;hpb=4e665c174de86f7fb68b257ccb2b0aa2d62cb429;p=jalview.git
diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index 03b94d3..b39d1dd 100644
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -1,25 +1,34 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview 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 3 of the License, or (at your option) any later version.
- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* Jalview 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 Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.commands;
-import java.util.*;
+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 jalview.datamodel.*;
+import java.util.Hashtable;
+import java.util.List;
/**
*
@@ -54,8 +63,8 @@ public class EditCommand implements CommandI
public static final int PASTE = 3;
public static final int REPLACE = 4;
-
- public static final int INSERT_NUC=5;
+
+ public static final int INSERT_NUC = 5;
Edit[] edits;
@@ -96,11 +105,13 @@ public class EditCommand implements CommandI
performEdit(0, null);
}
+ @Override
final public String getDescription()
{
return description;
}
+ @Override
public int getSize()
{
return edits == null ? 0 : edits.length;
@@ -194,42 +205,42 @@ public class EditCommand implements CommandI
case REPLACE:
replace(edits[e]);
break;
- //TODO:add deleteNuc for UNDO
- case INSERT_NUC:
- insertNuc(edits[e]);
- break;
+ // TODO:add deleteNuc for UNDO
+ // case INSERT_NUC:
+ // insertNuc(edits[e]);
+ // break;
}
}
}
+ @Override
final public void doCommand(AlignmentI[] views)
{
performEdit(0, views);
}
+ @Override
final public void undoCommand(AlignmentI[] views)
- {
- int e = 0, eSize = edits.length;
- for (e = eSize - 1; e > -1; e--)
- {
- switch (edits[e].command)
- {
- case INSERT_GAP:
- deleteGap(edits[e]);
- break;
- case DELETE_GAP:
- insertGap(edits[e]);
- break;
- case CUT:
- paste(edits[e], views);
- break;
- case PASTE:
- cut(edits[e], views);
- break;
- case REPLACE:
- replace(edits[e]);
- break;
- }
+ {
+ for(Edit e : edits){
+ 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;
+ }
}
}
@@ -240,23 +251,24 @@ 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);
}
-
- 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);
- }
+ //
+ // 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);
+ // }
final void deleteGap(Edit command)
{
@@ -344,8 +356,13 @@ public class EditCommand implements CommandI
// read it to the alignment
if (command.alIndex[i] < command.al.getHeight())
{
- command.al.getSequences().insertElementAt(command.seqs[i],
- command.alIndex[i]);
+ List sequences;
+ synchronized (sequences = command.al.getSequences())
+ {
+ // int index = command.al.findIndex(command.seqs[i]);
+ // sequences.add(index, command.seqs[i]);
+ sequences.add(command.alIndex[i] < 0 ? 0 : command.alIndex[i], command.seqs[i]);
+ }
}
else
{
@@ -387,9 +404,13 @@ public class EditCommand implements CommandI
+ command.number);
}
if (command.seqs[i].getStart() == start)
+ {
newstart--;
+ }
else
+ {
newend++;
+ }
}
}
command.string[i] = null;
@@ -446,6 +467,9 @@ public class EditCommand implements CommandI
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,
@@ -460,9 +484,48 @@ public class EditCommand implements CommandI
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;
}
@@ -651,10 +714,12 @@ public class EditCommand implements CommandI
{
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
{
@@ -733,8 +798,10 @@ public class EditCommand implements CommandI
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)