X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcommands%2FSlideSequencesCommand.java;h=153371a6baebd156d7f02f1e0cf88b7b4fd7044b;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=21385adf84c3ead4be6f9316888cf9a8e5eaebca;hpb=ea1bc94cb0d4ea4b877101cb7d93283ed4a199fe;p=jalview.git

diff --git a/src/jalview/commands/SlideSequencesCommand.java b/src/jalview/commands/SlideSequencesCommand.java
index 21385ad..153371a 100644
--- a/src/jalview/commands/SlideSequencesCommand.java
+++ b/src/jalview/commands/SlideSequencesCommand.java
@@ -1,93 +1,93 @@
-
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2007 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.*;
-
-public class SlideSequencesCommand extends EditCommand
-{
-  boolean gapsInsertedBegin = false;
-
-  public SlideSequencesCommand(String description,
-                               SequenceI[] seqsLeft,
-                               SequenceI[] seqsRight,
-                               int slideSize,
-                               char gapChar)
-  {
-    this.description = description;
-
-    int lSize = seqsLeft.length;
-    gapsInsertedBegin = false;
-    int i, j;
-    for (i = 0; i < lSize; i++)
-    {
-      for (j = 0; j < slideSize; j++)
-        if (!jalview.util.Comparison.isGap(seqsLeft[i].getCharAt(j)))
-        {
-          gapsInsertedBegin = true;
-          break;
-        }
-    }
-
-    if (!gapsInsertedBegin)
-      edits = new Edit[]
-          {  new Edit(DELETE_GAP, seqsLeft, 0, slideSize, gapChar)};
-    else
-      edits = new Edit[]
-          {  new Edit(INSERT_GAP, seqsRight, 0, slideSize, gapChar)};
-
-    performEdit(0);
-  }
-
-  public boolean getGapsInsertedBegin()
-  {
-    return gapsInsertedBegin;
-  }
-
-  public boolean appendSlideCommand(SlideSequencesCommand command)
-  {
-    boolean same = false;
-
-    if(command.edits[0].seqs.length==edits[0].seqs.length)
-    {
-      same = true;
-      for (int i = 0; i < command.edits[0].seqs.length; i++)
-      {
-        if (edits[0].seqs[i] != command.edits[0].seqs[i])
-        {
-          same = false;
-        }
-      }
-    }
-
-    if(same)
-    {
-      Edit[] temp = new Edit[command.edits.length + 1];
-      System.arraycopy(command.edits, 0, temp, 0, command.edits.length);
-      command.edits = temp;
-      command.edits[command.edits.length - 1] = edits[0];
-    }
-
-    return same;
-  }
-}
-
-
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.
+ *  
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.commands;
+
+import jalview.datamodel.SequenceI;
+
+public class SlideSequencesCommand extends EditCommand
+{
+  boolean gapsInsertedBegin = false;
+
+  public SlideSequencesCommand(String description, SequenceI[] seqsLeft,
+          SequenceI[] seqsRight, int slideSize, char gapChar)
+  {
+    this.description = description;
+
+    int lSize = seqsLeft.length;
+    gapsInsertedBegin = false;
+    int i, j;
+    for (i = 0; i < lSize; i++)
+    {
+      for (j = 0; j < slideSize; j++)
+      {
+        if (!jalview.util.Comparison.isGap(seqsLeft[i].getCharAt(j)))
+        {
+          gapsInsertedBegin = true;
+          break;
+        }
+      }
+    }
+
+    Edit e = null;
+
+    if (!gapsInsertedBegin)
+    {
+      e = new Edit(Action.DELETE_GAP, seqsLeft, 0, slideSize, gapChar);
+      setEdit(e);
+    }
+    else
+    {
+      e = new Edit(Action.INSERT_GAP, seqsRight, 0, slideSize, gapChar);
+      setEdit(e);
+    }
+
+    performEdit(e, null);
+  }
+
+  public boolean getGapsInsertedBegin()
+  {
+    return gapsInsertedBegin;
+  }
+
+  public boolean appendSlideCommand(SlideSequencesCommand command)
+  {
+    boolean same = false;
+
+    if (command.getEdit(0).seqs.length == getEdit(0).seqs.length)
+    {
+      same = true;
+      for (int i = 0; i < command.getEdit(0).seqs.length; i++)
+      {
+        if (getEdit(0).seqs[i] != command.getEdit(0).seqs[i])
+        {
+          same = false;
+        }
+      }
+    }
+
+    if (same)
+    {
+      command.addEdit(getEdit(0));
+    }
+
+    return same;
+  }
+}