X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcommands%2FChangeCaseCommand.java;h=b68b47c30bfe63e398c8923060499523bc006a3e;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=49faa50ec476d2202514cdbcbe0ad97c766edb2a;hpb=0c40653e5033e68c8d87955ea9f96879c8114b62;p=jalview.git

diff --git a/src/jalview/commands/ChangeCaseCommand.java b/src/jalview/commands/ChangeCaseCommand.java
index 49faa50..b68b47c 100644
--- a/src/jalview/commands/ChangeCaseCommand.java
+++ b/src/jalview/commands/ChangeCaseCommand.java
@@ -1,122 +1,143 @@
-  /*
- * 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
- */
-package jalview.commands;
-
-import jalview.datamodel.*;
-
-public class ChangeCaseCommand implements CommandI
-{
-  String description;
-  public static int TO_LOWER = 0;
-  public static int TO_UPPER = 1;
-  public static int TOGGLE_CASE = 2;
-  int caseChange = -1;
-  SequenceI [] seqs;
-  int [][] regions;
-  public ChangeCaseCommand(String description,
-                           SequenceI[] seqs,
-                           int [][] regions,
-                           int caseChange)
-  {
-    this.description = description;
-    this.seqs = seqs;
-    this.regions = regions;
-    this.caseChange = caseChange;
-    doCommand();
-  }
-
-  public String getDescription()
-  {
-    return description;
-  }
-
-  public int getSize()
-  {
-    return 1;
-  }
-
-  public void doCommand()
-  {
-    changeCase(true);
-  }
-
-  public void undoCommand()
-  {
-    changeCase(false);
-  }
-
-  void changeCase(boolean doCommand)
-  {
-    String sequence;
-    int start, end;
-    char nextChar;
-    for (int r = 0; r < regions.length; r++)
-    {
-      start = regions[r][0];
-      for (int s = 0; s < seqs.length; s++)
-      {
-        sequence = seqs[s].getSequence();
-        StringBuffer newSeq = new StringBuffer();
-
-        if (regions[r][1] > sequence.length())
-          end = sequence.length();
-        else
-          end = regions[r][1];
-
-        if (start > 0)
-        {
-          newSeq.append(sequence.substring(0, start));
-        }
-
-        if ( (caseChange == TO_UPPER && doCommand)
-            || (caseChange == TO_LOWER && !doCommand))
-          newSeq.append(sequence.substring(start, end).toUpperCase());
-
-        else if ( (caseChange == TO_LOWER && doCommand)
-                 || (caseChange == TO_UPPER && !doCommand))
-          newSeq.append(sequence.substring(start, end).toLowerCase());
-
-        else //TOGGLE CASE
-        {
-          for (int c = start; c < end; c++)
-          {
-            nextChar = sequence.charAt(c);
-            if ('a' <= nextChar && nextChar <= 'z')
-            {
-              // TO UPPERCASE !!!
-              nextChar -= ('a' - 'A');
-            }
-            else if ('A' <= nextChar && nextChar <= 'Z')
-            {
-              // TO LOWERCASE !!!
-              nextChar += ('a' - 'A');
-            }
-            newSeq.append(nextChar);
-          }
-        }
-
-        if (end < sequence.length())
-          newSeq.append(sequence.substring(end));
-
-        seqs[s].setSequence(newSeq.toString());
-      }
-    }
-  }
-
-}
+/*
+ * 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.AlignmentI;
+import jalview.datamodel.SequenceI;
+
+import java.util.List;
+
+public class ChangeCaseCommand implements CommandI
+{
+  String description;
+
+  public static int TO_LOWER = 0;
+
+  public static int TO_UPPER = 1;
+
+  public static int TOGGLE_CASE = 2;
+
+  int caseChange = -1;
+
+  SequenceI[] seqs;
+
+  List<int[]> regions;
+
+  public ChangeCaseCommand(String description, SequenceI[] seqs,
+          List<int[]> regions, int caseChange)
+  {
+    this.description = description;
+    this.seqs = seqs;
+    this.regions = regions;
+    this.caseChange = caseChange;
+    doCommand(null);
+  }
+
+  public String getDescription()
+  {
+    return description;
+  }
+
+  public int getSize()
+  {
+    return 1;
+  }
+
+  public void doCommand(AlignmentI[] views)
+  {
+    changeCase(true);
+  }
+
+  public void undoCommand(AlignmentI[] views)
+  {
+    changeCase(false);
+  }
+
+  void changeCase(boolean doCommand)
+  {
+    String sequence;
+    int start, end;
+    char nextChar;
+    for (int[] r : regions)
+    {
+      start = r[0];
+      for (int s = 0; s < seqs.length; s++)
+      {
+        sequence = seqs[s].getSequenceAsString();
+        StringBuffer newSeq = new StringBuffer();
+
+        if (r[1] > sequence.length())
+        {
+          end = sequence.length();
+        }
+        else
+        {
+          end = r[1];
+        }
+
+        if (start > 0)
+        {
+          newSeq.append(sequence.substring(0, start));
+        }
+
+        if ((caseChange == TO_UPPER && doCommand)
+                || (caseChange == TO_LOWER && !doCommand))
+        {
+          newSeq.append(sequence.substring(start, end).toUpperCase());
+        }
+
+        else if ((caseChange == TO_LOWER && doCommand)
+                || (caseChange == TO_UPPER && !doCommand))
+        {
+          newSeq.append(sequence.substring(start, end).toLowerCase());
+        }
+
+        else
+        // TOGGLE CASE
+        {
+          for (int c = start; c < end; c++)
+          {
+            nextChar = sequence.charAt(c);
+            if ('a' <= nextChar && nextChar <= 'z')
+            {
+              // TO UPPERCASE !!!
+              nextChar -= ('a' - 'A');
+            }
+            else if ('A' <= nextChar && nextChar <= 'Z')
+            {
+              // TO LOWERCASE !!!
+              nextChar += ('a' - 'A');
+            }
+            newSeq.append(nextChar);
+          }
+        }
+
+        if (end < sequence.length())
+        {
+          newSeq.append(sequence.substring(end));
+        }
+
+        seqs[s].setSequence(newSeq.toString());
+      }
+    }
+  }
+
+}