[Obo-svn-commit] SF.net SVN: obo: [223] phenote/trunk/src/java/phenote

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

Revision: 223
          http://svn.sourceforge.net/obo/?rev=223&view=rev
Author:   mgibson
Date:     2006-11-22 16:41:22 -0800 (Wed, 22 Nov 2006)

Log Message:
-----------
ammended pheno syntax adapter a little - still problems
pheno xml is still broken with new paradigm

Modified Paths:
--------------
    phenote/trunk/src/java/phenote/dataadapter/phenosyntax/PhenoSyntaxChar.java
    phenote/trunk/src/java/phenote/datamodel/Character.java
    phenote/trunk/src/java/phenote/datamodel/CharacterI.java

Modified: phenote/trunk/src/java/phenote/dataadapter/phenosyntax/PhenoSyntaxChar.java
===================================================================
--- phenote/trunk/src/java/phenote/dataadapter/phenosyntax/PhenoSyntaxChar.java	2006-11-22 23:40:05 UTC (rev 222)
+++ phenote/trunk/src/java/phenote/dataadapter/phenosyntax/PhenoSyntaxChar.java	2006-11-23 00:41:22 UTC (rev 223)
@@ -46,22 +46,31 @@
     }
     StringBuffer sb = new StringBuffer();
 
-    if (character.hasPub())
-      sb.append("PUB=").append(character.getPub());
-    // Genotype - not strictly part of pheno syntax but lets face it we need it
-    // i would say its an omission from syntax
-    sb.append(" GT=").append(character.getGenotype());
-    if (character.hasGeneticContext())
-      sb.append(" GC=").append(makeValue(character.getGeneticContext()));
+    try {
 
-    if (character.getEntity() == null)
-      throw new BadCharException("Error: character has no entity, ignoring");
-    sb.append(" E=").append(makeValue(character.getEntity()));
-
-    if (character.getQuality() == null)
-      throw new BadCharException("Error: character has no quality, ignoring");
-    sb.append(" Q=").append(makeValue(character.getQuality()));
-
+      if (character.hasValue("Pub")) // hasPub
+        sb.append("PUB=").append(character.getValueString("Pub")); //Pub());
+      // Genotype - not strictly part of pheno syntax but lets face it we need it
+      // i would say its an omission from syntax
+      //sb.append(" GT=").append(character.getGenotype());
+      sb.append(" GT=").append(character.getValueString("Genotype"));
+      if (character.hasValue("Genetic Context"))
+        sb.append(" GC=").append(makeValue(character.getTerm("Genetic Context")));
+      
+      if (!character.hasValue("Entity"))
+        throw new BadCharException("Error: character has no entity, ignoring");
+      //sb.append(" E=").append(makeValue(character.getEntity()));
+      sb.append(" E=").append(makeValue(character.getTerm("Entity")));
+      
+      //if (character.getQuality() == null)
+      if (!character.hasValue("Quality"))
+        throw new BadCharException("Error: character has no quality, ignoring");
+      sb.append(" Q=").append(makeValue(character.getTerm("Quality")));
+      
+    }
+    catch (Exception e) {
+      throw new BadCharException(e.getMessage());
+    }
     return sb.toString();
   }
 
@@ -77,20 +86,20 @@
     return term.getID() + " /*" + term.getName() + "*/";
   }
 
-  /** Merges id prefix and name, so for id GO:1234 with name "growth" returns
-      "GO:growth", which is readable and computable & syn acceptable - pase - doing ids*/
-  private String idPrefixAndName(OBOClass term) {
-    return getIdPrefix(term)+term.getName();
-  }
+//   /** Merges id prefix and name, so for id GO:1234 with name "growth" returns
+//       "GO:growth", which is readable and computable & syn acceptable - pase - doing ids*/
+//   private String idPrefixAndName(OBOClass term) {
+//     return getIdPrefix(term)+term.getName();
+//   }
     
 
-  /** for GO:12345 returns GO: - with colon! - pase - doing ids */
-  private String getIdPrefix(OBOClass term) {
-    if (term == null) return ""; // shouldnt happen
-    String id = term.getID();
-    int colonIndex = id.indexOf(":");
-    return id.substring(0,colonIndex+1); // +1 retain colon
-  }
+//   /** for GO:12345 returns GO: - with colon! - pase - doing ids */
+//   private String getIdPrefix(OBOClass term) {
+//     if (term == null) return ""; // shouldnt happen
+//     String id = term.getID();
+//     int colonIndex = id.indexOf(":");
+//     return id.substring(0,colonIndex+1); // +1 retain colon
+//   }
 
 
 

Modified: phenote/trunk/src/java/phenote/datamodel/Character.java
===================================================================
--- phenote/trunk/src/java/phenote/datamodel/Character.java	2006-11-22 23:40:05 UTC (rev 222)
+++ phenote/trunk/src/java/phenote/datamodel/Character.java	2006-11-23 00:41:22 UTC (rev 223)
@@ -42,13 +42,37 @@
 //       cfv = cf.getCharFieldEnum().getValue(this);
     return cfv;
   }
+
+  public String getValueString(String field) throws Exception {
+    CharField cf = getCharFieldForName(field); // throws ex
+    if (!hasValue(cf)) return null; // ?? exception?
+    return getValue(cf).getName();
+  }
+
+  public OBOClass getTerm(String field) throws Exception {
+    CharField cf = getCharFieldForName(field); // throws ex
+    if (!hasValue(cf)) return null; // ?? exception?
+    return getValue(cf).getOboClass();
+  }
+
   // should this be isNull?
   public boolean hasValue(CharField cf) {
     // empty string is a valid value for non-required field - or should there
     // be some sort of somthing to indicate "empty" value?
     return getValue(cf) != null; // && !getValue(cf).equals("");
   }
+  public boolean hasValue(String fieldName) throws Exception {
+    return hasValue(getCharFieldForName(fieldName));
+  }
 
+  private CharField getCharFieldForName(String fieldName) throws Exception {
+    for (CharField cf : charFieldToValue.keySet()) {
+      if (cf.getName().equalsIgnoreCase(fieldName))
+        return cf;
+    }
+    throw new Exception("No field for "+fieldName);
+  }
+
   public String getPub() { return pub; }
   public boolean hasPub() { return pub!=null && !pub.equals(""); }
   public String getGenotype() { return genotype; }

Modified: phenote/trunk/src/java/phenote/datamodel/CharacterI.java
===================================================================
--- phenote/trunk/src/java/phenote/datamodel/CharacterI.java	2006-11-22 23:40:05 UTC (rev 222)
+++ phenote/trunk/src/java/phenote/datamodel/CharacterI.java	2006-11-23 00:41:22 UTC (rev 223)
@@ -34,7 +34,11 @@
   /** generic fields!!! */
   public void setValue(CharField cf, CharFieldValue cfv); // ??
   public CharFieldValue getValue(CharField cf);
+  // should make an exception for this
+  public String getValueString(String fieldName) throws Exception; // yuck
+  public OBOClass getTerm(String field) throws Exception;
   public boolean hasValue(CharField cf);
+  public boolean hasValue(String fieldName) throws Exception;
   
   public CharacterI cloneCharacter();
   public boolean equals(CharacterI c);


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