refactored do and undo() method to take array of alignments for operations that resul...

[jalview.git] / src / jalview / commands / SlideSequencesCommand.java

diff --git a/src/jalview/commands/SlideSequencesCommand.java b/src/jalview/commands/SlideSequencesCommand.java
index 21385ad..9b9c99e 100644 (file)
--- a/src/jalview/commands/SlideSequencesCommand.java
+++ b/src/jalview/commands/SlideSequencesCommand.java
@@ -1,93 +1,93 @@
-\r
-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
-*/\r
-\r
-package jalview.commands;\r
-\r
-import jalview.datamodel.*;\r
-\r
-public class SlideSequencesCommand extends EditCommand\r
-{\r
-  boolean gapsInsertedBegin = false;\r
-\r
-  public SlideSequencesCommand(String description,\r
-                               SequenceI[] seqsLeft,\r
-                               SequenceI[] seqsRight,\r
-                               int slideSize,\r
-                               char gapChar)\r
-  {\r
-    this.description = description;\r
-\r
-    int lSize = seqsLeft.length;\r
-    gapsInsertedBegin = false;\r
-    int i, j;\r
-    for (i = 0; i < lSize; i++)\r
-    {\r
-      for (j = 0; j < slideSize; j++)\r
-        if (!jalview.util.Comparison.isGap(seqsLeft[i].getCharAt(j)))\r
-        {\r
-          gapsInsertedBegin = true;\r
-          break;\r
-        }\r
-    }\r
-\r
-    if (!gapsInsertedBegin)\r
-      edits = new Edit[]\r
-          {  new Edit(DELETE_GAP, seqsLeft, 0, slideSize, gapChar)};\r
-    else\r
-      edits = new Edit[]\r
-          {  new Edit(INSERT_GAP, seqsRight, 0, slideSize, gapChar)};\r
-\r
-    performEdit(0);\r
-  }\r
-\r
-  public boolean getGapsInsertedBegin()\r
-  {\r
-    return gapsInsertedBegin;\r
-  }\r
-\r
-  public boolean appendSlideCommand(SlideSequencesCommand command)\r
-  {\r
-    boolean same = false;\r
-\r
-    if(command.edits[0].seqs.length==edits[0].seqs.length)\r
-    {\r
-      same = true;\r
-      for (int i = 0; i < command.edits[0].seqs.length; i++)\r
-      {\r
-        if (edits[0].seqs[i] != command.edits[0].seqs[i])\r
-        {\r
-          same = false;\r
-        }\r
-      }\r
-    }\r
-\r
-    if(same)\r
-    {\r
-      Edit[] temp = new Edit[command.edits.length + 1];\r
-      System.arraycopy(command.edits, 0, temp, 0, command.edits.length);\r
-      command.edits = temp;\r
-      command.edits[command.edits.length - 1] = edits[0];\r
-    }\r
-\r
-    return same;\r
-  }\r
-}\r
-\r
-\r
+
+/*
+* 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,null);
+  }
+
+  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;
+  }
+}
+
+