X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcommands%2FTrimRegionCommand.java;h=2de353971033edba2c6554d03b4f10e9b91615b8;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=4c1dea0f26420edc314b79792864768bcfb356f0;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git

diff --git a/src/jalview/commands/TrimRegionCommand.java b/src/jalview/commands/TrimRegionCommand.java
index 4c1dea0..2de3539 100644
--- a/src/jalview/commands/TrimRegionCommand.java
+++ b/src/jalview/commands/TrimRegionCommand.java
@@ -1,178 +1,171 @@
-/*
- * 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 java.util.*;
-
-import jalview.datamodel.*;
-import jalview.util.*;
-
-public class TrimRegionCommand
-    extends EditCommand
-{
-  public static String TRIM_LEFT = "TrimLeft";
-  public static String TRIM_RIGHT = "TrimRight";
-
-  public ColumnSelection colSel = null;
-
-  int[] start;
-
-  ShiftList shiftList;
-
-  SequenceGroup selectionGroup;
-
-  Vector deletedHiddenColumns;
-
-  int columnsDeleted;
-
-  public TrimRegionCommand(String description,
-                           String command,
-                           SequenceI[] seqs,
-                           int column,
-                           AlignmentI al,
-                           ColumnSelection colSel,
-                           SequenceGroup selectedRegion)
-  {
-    this.description = description;
-    this.selectionGroup = selectedRegion;
-    this.colSel = colSel;
-    if (command.equalsIgnoreCase(TRIM_LEFT))
-    {
-      if (column == 0)
-      {
-        return;
-      }
-
-      columnsDeleted = column;
-
-      edits = new Edit[]
-          {
-          new Edit(CUT, seqs, 0, column, al)};
-    }
-    else if (command.equalsIgnoreCase(TRIM_RIGHT))
-    {
-      int width = al.getWidth() - column - 1;
-      if (width < 2)
-      {
-        return;
-      }
-
-      columnsDeleted = width - 1;
-
-      edits = new Edit[]
-          {
-          new Edit(CUT, seqs, column + 1, width, al)};
-    }
-
-    //We need to keep a record of the sequence start
-    //in order to restore the state after a redo
-    int i, isize = edits[0].seqs.length;
-    start = new int[isize];
-    for (i = 0; i < isize; i++)
-    {
-      start[i] = edits[0].seqs[i].getStart();
-    }
-
-    performEdit(0);
-  }
-
-  void cut(Edit command)
-  {
-    int column, j, jSize = command.seqs.length;
-    for (j = 0; j < jSize; j++)
-    {
-      if (command.position == 0)
-      {
-        //This is a TRIM_LEFT command
-        column = command.seqs[j].findPosition(command.number);
-        command.seqs[j].setStart(column);
-      }
-      else
-      {
-        //This is a TRIM_RIGHT command
-        column = command.seqs[j].findPosition(command.position) - 1;
-        command.seqs[j].setEnd(column);
-      }
-    }
-
-    super.cut(command);
-
-    if (command.position == 0)
-    {
-      deletedHiddenColumns = colSel.compensateForEdit(0, command.number);
-      if (selectionGroup != null)
-      {
-        selectionGroup.adjustForRemoveLeft(command.number);
-      }
-    }
-    else
-    {
-      deletedHiddenColumns = colSel.compensateForEdit(command.position,
-          command.number);
-      if (selectionGroup != null)
-      {
-        selectionGroup.adjustForRemoveRight(command.position);
-      }
-    }
-  }
-
-  void paste(Edit command)
-  {
-    super.paste(command);
-    int column, j, jSize = command.seqs.length;
-    for (j = 0; j < jSize; j++)
-    {
-      if (command.position == 0)
-      {
-        command.seqs[j].setStart(start[j]);
-      }
-      else
-      {
-        column = command.seqs[j]
-            .findPosition(command.number + command.position) - 1;
-        command.seqs[j].setEnd(column);
-      }
-    }
-
-    if (command.position == 0)
-    {
-      colSel.compensateForEdit(0, -command.number);
-      if (selectionGroup != null)
-      {
-        selectionGroup.adjustForRemoveLeft( -command.number);
-      }
-    }
-
-    if (deletedHiddenColumns != null)
-    {
-      int[] region;
-      for (int i = 0; i < deletedHiddenColumns.size(); i++)
-      {
-        region = (int[]) deletedHiddenColumns.elementAt(i);
-        colSel.hideColumns(region[0], region[1]);
-      }
-    }
-  }
-
-  public int getSize()
-  {
-    return columnsDeleted;
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 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;
+
+import java.util.*;
+
+import jalview.datamodel.*;
+import jalview.util.*;
+
+public class TrimRegionCommand extends EditCommand
+{
+  public static String TRIM_LEFT = "TrimLeft";
+
+  public static String TRIM_RIGHT = "TrimRight";
+
+  public ColumnSelection colSel = null;
+
+  int[] start;
+
+  ShiftList shiftList;
+
+  SequenceGroup selectionGroup;
+
+  Vector deletedHiddenColumns;
+
+  int columnsDeleted;
+
+  public TrimRegionCommand(String description, String command,
+          SequenceI[] seqs, int column, AlignmentI al,
+          ColumnSelection colSel, SequenceGroup selectedRegion)
+  {
+    this.description = description;
+    this.selectionGroup = selectedRegion;
+    this.colSel = colSel;
+    if (command.equalsIgnoreCase(TRIM_LEFT))
+    {
+      if (column == 0)
+      {
+        return;
+      }
+
+      columnsDeleted = column;
+
+      edits = new Edit[]
+      { new Edit(CUT, seqs, 0, column, al) };
+    }
+    else if (command.equalsIgnoreCase(TRIM_RIGHT))
+    {
+      int width = al.getWidth() - column - 1;
+      if (width < 2)
+      {
+        return;
+      }
+
+      columnsDeleted = width - 1;
+
+      edits = new Edit[]
+      { new Edit(CUT, seqs, column + 1, width, al) };
+    }
+
+    // We need to keep a record of the sequence start
+    // in order to restore the state after a redo
+    int i, isize = edits[0].seqs.length;
+    start = new int[isize];
+    for (i = 0; i < isize; i++)
+    {
+      start[i] = edits[0].seqs[i].getStart();
+    }
+
+    performEdit(0, null);
+  }
+
+  void cut(Edit command)
+  {
+    int column, j, jSize = command.seqs.length;
+    for (j = 0; j < jSize; j++)
+    {
+      if (command.position == 0)
+      {
+        // This is a TRIM_LEFT command
+        column = command.seqs[j].findPosition(command.number);
+        command.seqs[j].setStart(column);
+      }
+      else
+      {
+        // This is a TRIM_RIGHT command
+        column = command.seqs[j].findPosition(command.position) - 1;
+        command.seqs[j].setEnd(column);
+      }
+    }
+
+    super.cut(command, null);
+
+    if (command.position == 0)
+    {
+      deletedHiddenColumns = colSel.compensateForEdit(0, command.number);
+      if (selectionGroup != null)
+      {
+        selectionGroup.adjustForRemoveLeft(command.number);
+      }
+    }
+    else
+    {
+      deletedHiddenColumns = colSel.compensateForEdit(command.position,
+              command.number);
+      if (selectionGroup != null)
+      {
+        selectionGroup.adjustForRemoveRight(command.position);
+      }
+    }
+  }
+
+  void paste(Edit command)
+  {
+    super.paste(command, null);
+    int column, j, jSize = command.seqs.length;
+    for (j = 0; j < jSize; j++)
+    {
+      if (command.position == 0)
+      {
+        command.seqs[j].setStart(start[j]);
+      }
+      else
+      {
+        column = command.seqs[j].findPosition(command.number
+                + command.position) - 1;
+        command.seqs[j].setEnd(column);
+      }
+    }
+
+    if (command.position == 0)
+    {
+      colSel.compensateForEdit(0, -command.number);
+      if (selectionGroup != null)
+      {
+        selectionGroup.adjustForRemoveLeft(-command.number);
+      }
+    }
+
+    if (deletedHiddenColumns != null)
+    {
+      int[] region;
+      for (int i = 0; i < deletedHiddenColumns.size(); i++)
+      {
+        region = (int[]) deletedHiddenColumns.elementAt(i);
+        colSel.hideColumns(region[0], region[1]);
+      }
+    }
+  }
+
+  public int getSize()
+  {
+    return columnsDeleted;
+  }
+
+}