- /*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 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
-package jalview.commands;\r
-\r
-import jalview.datamodel.*;\r
-\r
-public class ChangeCaseCommand implements CommandI\r
-{\r
- String description;\r
- public static int TO_LOWER = 0;\r
- public static int TO_UPPER = 1;\r
- public static int TOGGLE_CASE = 2;\r
- int caseChange = -1;\r
- SequenceI [] seqs;\r
- int [][] regions;\r
- public ChangeCaseCommand(String description,\r
- SequenceI[] seqs,\r
- int [][] regions,\r
- int caseChange)\r
- {\r
- this.description = description;\r
- this.seqs = seqs;\r
- this.regions = regions;\r
- this.caseChange = caseChange;\r
- doCommand();\r
- }\r
-\r
- public String getDescription()\r
- {\r
- return description;\r
- }\r
-\r
- public int getSize()\r
- {\r
- return 1;\r
- }\r
-\r
- public void doCommand()\r
- {\r
- changeCase(true);\r
- }\r
-\r
- public void undoCommand()\r
- {\r
- changeCase(false);\r
- }\r
-\r
- void changeCase(boolean doCommand)\r
- {\r
- String sequence;\r
- int start, end;\r
- char nextChar;\r
- for (int r = 0; r < regions.length; r++)\r
- {\r
- start = regions[r][0];\r
- for (int s = 0; s < seqs.length; s++)\r
- {\r
- sequence = seqs[s].getSequence();\r
- StringBuffer newSeq = new StringBuffer();\r
-\r
- if (regions[r][1] > sequence.length())\r
- end = sequence.length();\r
- else\r
- end = regions[r][1];\r
-\r
- if (start > 0)\r
- {\r
- newSeq.append(sequence.substring(0, start));\r
- }\r
-\r
- if ( (caseChange == TO_UPPER && doCommand)\r
- || (caseChange == TO_LOWER && !doCommand))\r
- newSeq.append(sequence.substring(start, end).toUpperCase());\r
-\r
- else if ( (caseChange == TO_LOWER && doCommand)\r
- || (caseChange == TO_UPPER && !doCommand))\r
- newSeq.append(sequence.substring(start, end).toLowerCase());\r
-\r
- else //TOGGLE CASE\r
- {\r
- for (int c = start; c < end; c++)\r
- {\r
- nextChar = sequence.charAt(c);\r
- if ('a' <= nextChar && nextChar <= 'z')\r
- {\r
- // TO UPPERCASE !!!\r
- nextChar -= ('a' - 'A');\r
- }\r
- else if ('A' <= nextChar && nextChar <= 'Z')\r
- {\r
- // TO LOWERCASE !!!\r
- nextChar += ('a' - 'A');\r
- }\r
- newSeq.append(nextChar);\r
- }\r
- }\r
-\r
- if (end < sequence.length())\r
- newSeq.append(sequence.substring(end));\r
-\r
- seqs[s].setSequence(newSeq.toString());\r
- }\r
- }\r
- }\r
-\r
-}\r
+/*
+ * 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());
+ }
+ }
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff