[Obo-svn-commit] SF.net SVN: obo: [774] phenote/trunk/src/java/phenote/dataadapter

[<mg...@us...>]

Revision: 774
          http://obo.svn.sourceforge.net/obo/?rev=774&view=rev
Author:   mgibson
Date:     2007-07-26 11:07:38 -0700 (Thu, 26 Jul 2007)

Log Message:
-----------
made a FlyGenotypeGroupAdapter that makes fly genotype strings from fly group 
expects the fly genotype config fields
just implements makeNameFromChar from AbstractGroupAdapter

Modified Paths:
--------------
    phenote/trunk/src/java/phenote/dataadapter/AbstractGroupAdapter.java
    phenote/trunk/src/java/phenote/dataadapter/AllFieldsGroupAdapter.java

Added Paths:
-----------
    phenote/trunk/src/java/phenote/dataadapter/fly/FlyGenotypeGroupAdapter.java

Modified: phenote/trunk/src/java/phenote/dataadapter/AbstractGroupAdapter.java
===================================================================
--- phenote/trunk/src/java/phenote/dataadapter/AbstractGroupAdapter.java	2007-07-26 13:55:21 UTC (rev 773)
+++ phenote/trunk/src/java/phenote/dataadapter/AbstractGroupAdapter.java	2007-07-26 18:07:38 UTC (rev 774)
@@ -7,6 +7,7 @@
 import org.geneontology.oboedit.datamodel.Namespace;
 import org.geneontology.oboedit.datamodel.OBOClass;
 import org.geneontology.oboedit.datamodel.OBOSession;
+import org.geneontology.oboedit.datamodel.impl.OBOClassImpl;
 import org.geneontology.oboedit.datamodel.impl.OBOSessionImpl;
 
 import phenote.datamodel.CharField;
@@ -18,7 +19,7 @@
 import phenote.edit.CharChangeListener;
 import phenote.edit.CharChangeEvent;
 
-abstract class AbstractGroupAdapter implements GroupAdapterI {
+public abstract class AbstractGroupAdapter implements GroupAdapterI {
 
   private CharChangeListener charListener;
   private String group;
@@ -61,9 +62,20 @@
     getDestinationOntology().setOboSession(os);
   }
 
+  // protected? - subclass override?
+  protected OBOClass makeOboClassFromChar(CharacterI c) {
+    if (c.hasNoContent()) return null; // ex?
+    String name = makeNameFromChar(c);
+    String id = ":"+name;
+    OBOClass o = new OBOClassImpl(name,id);
+    o.setNamespace(getNamespace()); // ???
+    return o;
+  }
+
   /** This is where subclasses come in and do their thing */
-  protected abstract OBOClass makeOboClassFromChar(CharacterI c);
+  protected abstract String makeNameFromChar(CharacterI c); 
 
+
   public void setDestinationField(String fieldName) {
     try {
       destinationCharField = OntologyManager.inst().getCharFieldForName(fieldName);

Modified: phenote/trunk/src/java/phenote/dataadapter/AllFieldsGroupAdapter.java
===================================================================
--- phenote/trunk/src/java/phenote/dataadapter/AllFieldsGroupAdapter.java	2007-07-26 13:55:21 UTC (rev 773)
+++ phenote/trunk/src/java/phenote/dataadapter/AllFieldsGroupAdapter.java	2007-07-26 18:07:38 UTC (rev 774)
@@ -3,9 +3,6 @@
 
 import org.apache.log4j.Logger;
 
-import org.geneontology.oboedit.datamodel.OBOClass;
-import org.geneontology.oboedit.datamodel.impl.OBOClassImpl;
-
 import phenote.datamodel.CharField;
 import phenote.datamodel.CharacterI;
 
@@ -17,9 +14,8 @@
 
   // public boolean isFieldValueMaker() { return true; } ??
 
-  // protected? - subclass override?
-  protected OBOClass makeOboClassFromChar(CharacterI c) {
-    if (c.hasNoContent()) return null; // ex?
+
+  protected String makeNameFromChar(CharacterI c) {
     StringBuilder sb = new StringBuilder();
     for (CharField cf : c.getAllCharFields()) {
       if (c.hasValue(cf))
@@ -28,15 +24,9 @@
     if (sb.length() == 0) return null; //?
     sb.deleteCharAt(sb.length()-1);
     String name = sb.toString();
-    sb.insert(0,':');
-    String id = sb.toString();
-    OBOClass o = new OBOClassImpl(name,id);
-    o.setNamespace(getNamespace()); // ???
-    return o;
+    return name;
   }
 
-
-
   private Logger log;
   private Logger log() {
     if (log == null) log = Logger.getLogger(getClass());

Added: phenote/trunk/src/java/phenote/dataadapter/fly/FlyGenotypeGroupAdapter.java
===================================================================
--- phenote/trunk/src/java/phenote/dataadapter/fly/FlyGenotypeGroupAdapter.java	                        (rev 0)
+++ phenote/trunk/src/java/phenote/dataadapter/fly/FlyGenotypeGroupAdapter.java	2007-07-26 18:07:38 UTC (rev 774)
@@ -0,0 +1,43 @@
+package phenote.dataadapter.fly;
+
+import org.apache.log4j.Logger;
+
+import phenote.datamodel.CharacterI;
+import phenote.datamodel.CharFieldException;
+import phenote.dataadapter.AbstractGroupAdapter;
+
+/** Makes fly style genotype from locus allele 1, locus allele 2, non locus allele,
+    and accesories - with datatags LA1, LA2, NLA, ACC */
+
+public class FlyGenotypeGroupAdapter extends AbstractGroupAdapter {
+
+  public FlyGenotypeGroupAdapter(String group) {
+    super(group);
+  }
+  protected String makeNameFromChar(CharacterI c) {
+    StringBuilder sb = new StringBuilder();
+    try {
+      if (c.hasValue("LA1"))
+        sb.append(c.getValueString("LA1"));
+      if (c.hasValue("LA2"))
+        sb.append("/").append(c.getValueString("LA2"));
+      // eventually this will be a list
+      if (c.hasValue("NLA"))
+        sb.append(", ").append(c.getValueString("NLA"));
+      // this will also be a list
+      if (c.hasValue("ACC"))
+        sb.append(" { ").append(c.getValueString("ACC")).append(" }");
+      
+    } catch (CharFieldException e) {
+      log().error(e.getMessage());
+    }
+    return sb.toString();
+  }
+
+  private Logger log;
+  private Logger log() {
+    if (log == null) log = Logger.getLogger(getClass());
+    return log;
+  }
+
+}


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