X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcommands%2FRemoveGapColCommand.java;h=83197d7f6efc7da6ca2fd0d7b2c2afe176bb505f;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=5bf5b6100f5d005e47c9ca6ea26e431cfee62397;hpb=8787ad51b5206692859df9b84e836a01e7a91c02;p=jalview.git

diff --git a/src/jalview/commands/RemoveGapColCommand.java b/src/jalview/commands/RemoveGapColCommand.java
index 5bf5b61..83197d7 100644
--- a/src/jalview/commands/RemoveGapColCommand.java
+++ b/src/jalview/commands/RemoveGapColCommand.java
@@ -1,91 +1,116 @@
-package jalview.commands;
-  /*
- * 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
- */
-
-import jalview.datamodel.*;
-
-public class RemoveGapColCommand  extends EditCommand
-{
-  public RemoveGapColCommand(String description,
-                             SequenceI[] seqs,
-                             int start, int end, char gapChar)
-  {
-    this.description = description;
-
-    int j, jSize = seqs.length;
-
-    int startCol = -1, endCol = -1;
-    int deletedCols = 0;
-
-    edits = new Edit[0];
-
-    boolean delete = true;
-    for (int i = start; i < end; i++)
-    {
-      delete = true;
-
-      for (j = 0; j < jSize; j++)
-      {
-        if (seqs[j].getLength() > i)
-        {
-          if (!jalview.util.Comparison.isGap(seqs[j].getCharAt(i)))
-          {
-            if (delete)
-              endCol = i;
-
-            delete = false;
-            break;
-          }
-        }
-      }
-
-      if (delete && startCol == -1)
-      {
-        startCol = i;
-      }
-
-      if (!delete && startCol > -1)
-      {
-        this.appendEdit(DELETE_GAP, seqs,
-                        startCol - deletedCols,
-                        endCol - startCol,
-                        gapChar,
-                        false);
-
-        deletedCols += (endCol - startCol);
-        startCol = -1;
-        endCol = -1;
-      }
-    }
-
-    if (delete && startCol > -1)
-    {
-       //This is for empty columns at the
-       //end of the alignment
-      this.appendEdit(DELETE_GAP, seqs,
-                        startCol - deletedCols,
-                        end-startCol+1,
-                        gapChar,
-                        false);
-    }
-
-    performEdit(0);
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 
+ * 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/>.
+ */
+package jalview.commands;
+
+/*
+ * 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
+ */
+
+import jalview.datamodel.*;
+
+public class RemoveGapColCommand extends EditCommand
+{
+  int columnsDeleted;
+
+  public RemoveGapColCommand(String description, SequenceI[] seqs,
+          int start, int end, AlignmentI al)
+  {
+    this.description = description;
+
+    int j, jSize = seqs.length;
+
+    int startCol = -1, endCol = -1;
+    columnsDeleted = 0;
+
+    edits = new Edit[0];
+
+    boolean delete = true;
+    for (int i = start; i <= end; i++)
+    {
+      delete = true;
+
+      for (j = 0; j < jSize; j++)
+      {
+        if (seqs[j].getLength() > i)
+        {
+          if (!jalview.util.Comparison.isGap(seqs[j].getCharAt(i)))
+          {
+            if (delete)
+            {
+              endCol = i;
+            }
+
+            delete = false;
+            break;
+          }
+        }
+      }
+
+      if (delete && startCol == -1)
+      {
+        startCol = i;
+      }
+
+      if (!delete && startCol > -1)
+      {
+        this.appendEdit(DELETE_GAP, seqs, startCol - columnsDeleted, endCol
+                - startCol, al, false, null);
+
+        columnsDeleted += (endCol - startCol);
+        startCol = -1;
+        endCol = -1;
+      }
+    }
+
+    if (delete && startCol > -1)
+    {
+      // This is for empty columns at the
+      // end of the alignment
+
+      this.appendEdit(DELETE_GAP, seqs, startCol - columnsDeleted, end
+              - startCol + 1, al, false, null);
+
+      columnsDeleted += (end - startCol + 1);
+    }
+
+    performEdit(0, null);
+  }
+
+  public int getSize()
+  {
+    // We're interested in the number of columns deleted,
+    // Not the number of sequence edits.
+    return columnsDeleted;
+  }
+
+}