[MOBY-guts] biomoby commit
Eddie Kawas
kawas at pub.open-bio.org
Wed Dec 22 16:01:38 UTC 2004
kawas
Wed Dec 22 11:01:38 EST 2004
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool
In directory pub.open-bio.org:/tmp/cvs-serv2460/org/biomoby/client/gui/objectCreationTool
Modified Files:
TreeWindow.java PopUpWindow.java Registration.java
TreeMouseListener.java SubmissionWindow.java
Log Message:
Added documentation
moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool TreeWindow.java,1.1,1.2 PopUpWindow.java,1.1,1.2 Registration.java,1.1,1.2 TreeMouseListener.java,1.1,1.2 SubmissionWindow.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/TreeWindow.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/TreeWindow.java 2004/12/22 14:34:58 1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/TreeWindow.java 2004/12/22 16:01:38 1.2
@@ -16,8 +16,11 @@
import org.biomoby.client.gui.util.ObjectXMLWriter;
/**
* @author Eddie Kawas
- * <p>Created for
- * <p>This class was created to ...
+ * <p>This class was created with the purpose of
+ * displaying the mobycentral object ontology in
+ * tree format, as well as providing a way to
+ * retrieve information about objects from the
+ * mobycentral object ontology.
* <p>For questions, comments, or bugs
* <p>email me at edward.kawas at gmail.com
*/
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/PopUpWindow.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/PopUpWindow.java 2004/12/22 14:34:58 1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/PopUpWindow.java 2004/12/22 16:01:38 1.2
@@ -13,8 +13,8 @@
import javax.swing.ImageIcon;
/**
* @author Eddie Kawas
- * <p>Created for
- * <p>This class was created to ...
+ * <p>This class was created to present a convenience class
+ * that presents modal pop up windows to the user.
* <p>For questions, comments, or bugs
* <p>email me at edward.kawas at gmail.com
*/
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/Registration.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/Registration.java 2004/09/27 22:15:13 1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/Registration.java 2004/12/22 16:01:38 1.2
@@ -20,24 +20,47 @@
static final String ENDPOINT = "http://mobycentral.cbr.nrc.ca:8080/cgi-bin/MOBY05/mobycentral.pl";
static final String NAMESPACE = "http://mobycentral.cbr.nrc.ca:8080/MOBY/Central";
-
-
private static boolean PROTO = false;
+ /**
+ *
+ * <b><i>Constructor</i></b>
+ * @param name - the name of the moby data type
+ * @param proto - is this object a prototype?
+ */
public Registration(String name, boolean proto) {
super(name);
PROTO = proto;
}
+ /**
+ *
+ * <b>PRE:</b>None.<p>
+ * <b>POST:</b>The name of the data type is renamed to str.<p>
+ * @param str - the new name of the data type.
+ */
public void setName(String str) {
this.name = str;
}
-
+ /**
+ *
+ * <b>PRE:</b>Pair p is a well constructed Pair object.<p>
+ * <b>POST:</b>Data from Pair p is added to the data type
+ * in the form of HASA relationship<p>
+ * @param p - the pair to add to the HASA containment relationship for the data type
+ */
public void addHASAChildren(Pair p) {
//System.out.println("ArticleName: " + p.getArticlename() + " DataType: " + p.getAttribute());
this.addChild(p.getArticlename(), p.getAttribute(), Central.iHASA);
}
+ /**
+ *
+ * <b>PRE:</b>Pair p is a well constructed Pair object.<p>
+ * <b>POST:</b>Data from Pair p is added to the data type
+ * in the form of HAS relationship<p>
+ * @param p - the pair to add to the HAS containment relationship for the data type
+ */
public void addHASChildren(Pair p) {
//System.out.println("ArticleName: " + p.getArticlename() + " DataType: " + p.getAttribute());
this.addChild(p.getArticlename(), p.getAttribute(), Central.iHAS);
@@ -45,9 +68,11 @@
}
/**
- *
- * PRE:
- * <p>POST:</p>
+ *
+ * <b>PRE:</b>MobyDataType has been properly initialized.<p>
+ * <b>POST:</b>MobyDataType is registered in the mobycentral object
+ * ontology and a string representing its LSID is returned.<p>
+ * @param tool - the ObjectCreationTool that is registering this new data type.
* @return 1 for success, 0 for failure and -1 for 'pending curation'
*/
public String performRegistration(ObjectCreationTool tool) {
@@ -83,12 +108,10 @@
return reg;
}
+
/**
- *
- * PRE:
- * <p>POST:</p>
- * @param name
- * @return
+ * @deprecated - no longer used.
+ * TODO - remove method from class.
*/
public String getDataTypeInfo(String name) {
String ret = "";
@@ -108,10 +131,19 @@
}
+ /**
+ *
+ * <b>PRE:</b>MobyDataType has been registered.<p>
+ * <b>POST:</b>LSID is returned<p>
+ * @return - the LSID of the moby data type.
+ */
public String getMobyID() {
return this.getId();
}
+ /**
+ * TODO - remove from class. Shouldn't have this method.
+ */
public void setMobyID(String s) {
this.setId(s);
}
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/TreeMouseListener.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/TreeMouseListener.java 2004/12/22 14:34:58 1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/TreeMouseListener.java 2004/12/22 16:01:38 1.2
@@ -10,8 +10,11 @@
import javax.swing.tree.TreePath;
/**
- * @author Eddie Kawas <p>Created for <p>This class was created to ... <p>For
- * questions, comments, or bugs <p>email me at edward.kawas at gmail.com
+ * @author Eddie Kawas
+ * <p>This class was created to implement the Mouselistener interface
+ * for use with a tree that displays the mobycentral object ontology.
+ * <p>For questions, comments, or bugs
+ * <p>email me at edward.kawas at gmail.com
*/
public class TreeMouseListener implements MouseListener {
@@ -65,10 +68,11 @@
}
/**
- * <b>PRE: </b> <p><b>POST: </b> <p>
- *
- * @param selected
- * @return
+ * <b>PRE: </b> None.<p>
+ * <b>POST: </b> THe name of the event originator is returned: ISA, HAS, HASA.<p>
+ * @param selected - the integer value representing the event originator
+ * @see org.biomoby.client.gui.objectCreationTool
+ * @return String representing the event originator.
*/
private String getEventOriginatorName(int selected) {
String str = null;
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/SubmissionWindow.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/SubmissionWindow.java 2004/12/22 14:34:58 1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/SubmissionWindow.java 2004/12/22 16:01:38 1.2
@@ -13,8 +13,9 @@
import javax.swing.ImageIcon;
/**
* @author Eddie Kawas
- * <p>Created for
- * <p>This class was created to ...
+ * <p>This class was created to present a view to the user
+ * of the tool that displays their newly created object prior
+ * to registration.
* <p>For questions, comments, or bugs
* <p>email me at edward.kawas at gmail.com
*/
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