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Formatting changes
[jalview.git]
/
src
/
jalview
/
datamodel
/
SuperGroup.java
diff --git
a/src/jalview/datamodel/SuperGroup.java
b/src/jalview/datamodel/SuperGroup.java
index
ad6f703
..
b2993b5
100755
(executable)
--- a/
src/jalview/datamodel/SuperGroup.java
+++ b/
src/jalview/datamodel/SuperGroup.java
@@
-18,8
+18,6
@@
*/
\r
package jalview.datamodel;
\r
\r
*/
\r
package jalview.datamodel;
\r
\r
-import jalview.analysis.*;
\r
-
\r
import jalview.datamodel.*;
\r
\r
import jalview.schemes.*;
\r
import jalview.datamodel.*;
\r
\r
import jalview.schemes.*;
\r
@@
-27,15
+25,28
@@
import jalview.schemes.*;
import java.util.*;
\r
\r
\r
import java.util.*;
\r
\r
\r
-public class SuperGroup {
\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
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
public ColourSchemeI cs;
\r
Vector sequenceGroups = new Vector();
\r
\r
- public SuperGroup() {
\r
+ /**
\r
+ * Creates a new SuperGroup object.
\r
+ */
\r
+ public SuperGroup()
\r
+ {
\r
groupName = "Super group";
\r
this.displayBoxes = true;
\r
this.displayText = true;
\r
groupName = "Super group";
\r
this.displayBoxes = true;
\r
this.displayText = true;
\r
@@
-43,8
+54,18
@@
public class SuperGroup {
cs = null;
\r
}
\r
\r
cs = null;
\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
public SuperGroup(String groupName, ColourSchemeI scheme,
\r
- boolean displayBoxes, boolean displayText, boolean colourText) {
\r
+ boolean displayBoxes, boolean displayText, boolean colourText)
\r
+ {
\r
this.groupName = groupName;
\r
this.displayBoxes = displayBoxes;
\r
this.displayText = displayText;
\r
this.groupName = groupName;
\r
this.displayBoxes = displayBoxes;
\r
this.displayText = displayText;
\r
@@
-52,39
+73,80
@@
public class SuperGroup {
this.cs = scheme;
\r
}
\r
\r
this.cs = scheme;
\r
}
\r
\r
- public String getName() {
\r
+ /**
\r
+ * DOCUMENT ME!
\r
+ *
\r
+ * @return DOCUMENT ME!
\r
+ */
\r
+ public String getName()
\r
+ {
\r
return groupName;
\r
}
\r
\r
return groupName;
\r
}
\r
\r
- public void setName(String name) {
\r
+ /**
\r
+ * DOCUMENT ME!
\r
+ *
\r
+ * @param name DOCUMENT ME!
\r
+ */
\r
+ public void setName(String name)
\r
+ {
\r
groupName = name;
\r
}
\r
\r
groupName = name;
\r
}
\r
\r
- public void addGroup(SequenceGroup sg) {
\r
- if (!sequenceGroups.contains(sg)) {
\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
sequenceGroups.addElement(sg);
\r
}
\r
}
\r
\r
- public void addOrRemove(SequenceGroup sg) {
\r
- if (sequenceGroups.contains(sg)) {
\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
deleteGroup(sg);
\r
- } else {
\r
+ }
\r
+ else
\r
+ {
\r
addGroup(sg);
\r
}
\r
}
\r
\r
addGroup(sg);
\r
}
\r
}
\r
\r
- public void deleteGroup(SequenceGroup sg) {
\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
sequenceGroups.removeElement(sg);
\r
}
\r
\r
- public void setSuperGroupProperties(SequenceGroup sg) {
\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
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
+ 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
SequenceGroup temp = (SequenceGroup) sequenceGroups.elementAt(i);
\r
temp.cs = sg.cs;
\r
temp.colourText = sg.colourText;
\r
@@
-93,11
+155,25
@@
public class SuperGroup {
}
\r
}
\r
\r
}
\r
}
\r
\r
- public int getSize() {
\r
+ /**
\r
+ * DOCUMENT ME!
\r
+ *
\r
+ * @return DOCUMENT ME!
\r
+ */
\r
+ public int getSize()
\r
+ {
\r
return sequenceGroups.size();
\r
}
\r
\r
return sequenceGroups.size();
\r
}
\r
\r
- public SequenceGroup getGroupeAt(int i) {
\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
return (SequenceGroup) sequenceGroups.elementAt(i);
\r
}
\r
}
\r