+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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.datamodel;\r
\r
-import jalview.schemes.*;\r
-import jalview.analysis.*;\r
import jalview.datamodel.*;\r
+\r
+import jalview.schemes.*;\r
+\r
import java.util.*;\r
\r
+\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
public class SuperGroup\r
{\r
- String groupName;\r
- boolean displayBoxes;\r
- boolean displayText;\r
- boolean colourText;\r
- public ColourSchemeI cs;\r
- ArrayList sequenceGroups = new ArrayList();\r
-\r
- public SuperGroup()\r
- {\r
- groupName = "Super group";\r
- this.displayBoxes = true;\r
- this.displayText = true;\r
- this.colourText = false;\r
- cs = null;\r
- }\r
-\r
-\r
- public SuperGroup(String groupName, ColourSchemeI scheme,\r
- boolean displayBoxes, boolean displayText,\r
- boolean colourText)\r
- {\r
- this.groupName = groupName;\r
- this.displayBoxes = displayBoxes;\r
- this.displayText = displayText;\r
- this.colourText = colourText;\r
- this.cs = scheme;\r
- }\r
-\r
- public String getName()\r
- {\r
- return groupName;\r
- }\r
-\r
- public void setName(String name)\r
- {\r
- groupName = name;\r
- }\r
-\r
-\r
- public void addGroup(SequenceGroup sg)\r
- {\r
- if(!sequenceGroups.contains(sg))\r
- sequenceGroups.add(sg);\r
- }\r
-\r
- public void addOrRemove(SequenceGroup sg)\r
- {\r
- if(sequenceGroups.contains(sg))\r
- deleteGroup(sg);\r
- else\r
- addGroup(sg);\r
- }\r
-\r
- public void deleteGroup(SequenceGroup sg)\r
- {\r
- sequenceGroups.remove(sg);\r
- }\r
-\r
- public void setSuperGroupProperties(SequenceGroup sg)\r
- {\r
- cs = sg.cs;\r
- colourText = sg.colourText;\r
- displayText = sg.displayText;\r
- displayBoxes = sg.displayBoxes;\r
-\r
- for(int i=0; i<sequenceGroups.size(); i++)\r
+ String groupName;\r
+ boolean displayBoxes;\r
+ boolean displayText;\r
+ boolean colourText;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public ColourSchemeI cs;\r
+ Vector sequenceGroups = new Vector();\r
+\r
+ /**\r
+ * Creates a new SuperGroup object.\r
+ */\r
+ public SuperGroup()\r
{\r
- SequenceGroup temp = (SequenceGroup)sequenceGroups.get(i);\r
- temp.cs = sg.cs;\r
- temp.colourText = sg.colourText;\r
- temp.displayText = sg.displayText;\r
- temp.displayBoxes = sg.displayBoxes;\r
+ groupName = "Super group";\r
+ this.displayBoxes = true;\r
+ this.displayText = true;\r
+ this.colourText = false;\r
+ cs = null;\r
}\r
- }\r
\r
+ /**\r
+ * Creates a new SuperGroup object.\r
+ *\r
+ * @param groupName DOCUMENT ME!\r
+ * @param scheme DOCUMENT ME!\r
+ * @param displayBoxes DOCUMENT ME!\r
+ * @param displayText DOCUMENT ME!\r
+ * @param colourText DOCUMENT ME!\r
+ */\r
+ public SuperGroup(String groupName, ColourSchemeI scheme,\r
+ boolean displayBoxes, boolean displayText, boolean colourText)\r
+ {\r
+ this.groupName = groupName;\r
+ this.displayBoxes = displayBoxes;\r
+ this.displayText = displayText;\r
+ this.colourText = colourText;\r
+ this.cs = scheme;\r
+ }\r
\r
- public int getSize()\r
- {\r
- return sequenceGroups.size();\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String getName()\r
+ {\r
+ return groupName;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param name DOCUMENT ME!\r
+ */\r
+ public void setName(String name)\r
+ {\r
+ groupName = name;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param sg DOCUMENT ME!\r
+ */\r
+ public void addGroup(SequenceGroup sg)\r
+ {\r
+ if (!sequenceGroups.contains(sg))\r
+ {\r
+ sequenceGroups.addElement(sg);\r
+ }\r
+ }\r
\r
- public SequenceGroup getGroupeAt(int i)\r
- {\r
- return (SequenceGroup) sequenceGroups.get(i);\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param sg DOCUMENT ME!\r
+ */\r
+ public void addOrRemove(SequenceGroup sg)\r
+ {\r
+ if (sequenceGroups.contains(sg))\r
+ {\r
+ deleteGroup(sg);\r
+ }\r
+ else\r
+ {\r
+ addGroup(sg);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param sg DOCUMENT ME!\r
+ */\r
+ public void deleteGroup(SequenceGroup sg)\r
+ {\r
+ sequenceGroups.removeElement(sg);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param sg DOCUMENT ME!\r
+ */\r
+ public void setSuperGroupProperties(SequenceGroup sg)\r
+ {\r
+ cs = sg.cs;\r
+ colourText = sg.colourText;\r
+ displayText = sg.displayText;\r
+ displayBoxes = sg.displayBoxes;\r
+\r
+ for (int i = 0; i < sequenceGroups.size(); i++)\r
+ {\r
+ SequenceGroup temp = (SequenceGroup) sequenceGroups.elementAt(i);\r
+ temp.cs = sg.cs;\r
+ temp.colourText = sg.colourText;\r
+ temp.displayText = sg.displayText;\r
+ temp.displayBoxes = sg.displayBoxes;\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public int getSize()\r
+ {\r
+ return sequenceGroups.size();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param i DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public SequenceGroup getGroupeAt(int i)\r
+ {\r
+ return (SequenceGroup) sequenceGroups.elementAt(i);\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff