Removing version argument constructors that shouldn't be used. Temporary allow -- with global variant to indicate this should be removed -- header records without description fields. Real error checking in the headers.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3818 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broad/tribble/vcf/VCFCompoundHeaderLine.java

@@ -39,7 +39,6 @@ public abstract class VCFCompoundHeaderLine extends VCFHeaderLine implements VCF
         SupportedHeaderLineType(boolean flagValues) {
             allowFlagValues = flagValues;
         }
-
     }
 
     // the field types
@@ -79,15 +78,7 @@ public abstract class VCFCompoundHeaderLine extends VCFHeaderLine implements VCF
         this.type = type;
         this.description = description;
         this.lineType = lineType;
-    }
+        validate();
-
-    protected VCFCompoundHeaderLine(String name, int count, VCFHeaderLineType type, String description, SupportedHeaderLineType lineType, VCFHeaderVersion version) {
-        super(lineType.toString(), "");
-        this.name = name;
-        this.count = count;
-        this.type = type;
-        this.description = description;
-        this.lineType = lineType;
     }
 
     /**
@@ -107,8 +98,20 @@ public abstract class VCFCompoundHeaderLine extends VCFHeaderLine implements VCF
         type = VCFHeaderLineType.valueOf(mapping.get("Type"));
         if (type == VCFHeaderLineType.Flag && !allowFlagValues())
             throw new IllegalArgumentException("Flag is an unsupported type for this kind of field");
+
         description = mapping.get("Description");
+        if ( description == null && ALLOW_UNBOUND_DESCRIPTIONS ) // handle the case where there's no description provided
+            description = UNBOUND_DESCRIPTION;
+        
         this.lineType = lineType;
+
+        validate();
+    }
+
+    private void validate() {
+        if ( name == null || type == null || description == null || lineType == null )
+            throw new IllegalArgumentException(String.format("Invalid VCFCompoundHeaderLine: key=%s name=%s type=%s desc=%s lineType=%s", 
+                    super.getKey(), name, type, description, lineType ));
     }
 
     /**

java/src/org/broad/tribble/vcf/VCFFilterHeaderLine.java

@@ -25,6 +25,9 @@ public class VCFFilterHeaderLine extends VCFHeaderLine implements VCFNamedHeader
         super("FILTER", "");
         this.name = name;
         this.description = description;
+
+        if ( name == null || description == null )
+            throw new IllegalArgumentException(String.format("Invalid VCFCompoundHeaderLine: key=%s name=%s desc=%s", super.getKey(), name, description ));
     }
 
     /**
@@ -38,6 +41,8 @@ public class VCFFilterHeaderLine extends VCFHeaderLine implements VCFNamedHeader
         Map<String,String> mapping = VCFHeaderLineTranslator.parseLine(version,line, Arrays.asList("ID","Description"));
         name = mapping.get("ID");
         description = mapping.get("Description");
+        if ( description == null && ALLOW_UNBOUND_DESCRIPTIONS ) // handle the case where there's no description provided 
+            description = UNBOUND_DESCRIPTION;
     }
 
     protected String toStringEncoding() {

java/src/org/broad/tribble/vcf/VCFHeaderLine.java

@@ -38,8 +38,9 @@ import java.util.Map;
  *         A class representing a key=value entry in the VCF header
  */
 public class VCFHeaderLine implements Comparable {
+    protected static boolean ALLOW_UNBOUND_DESCRIPTIONS = true;
+    protected static String UNBOUND_DESCRIPTION = "Not provided in original VCF header";
 
-    private String stringRep = null;
     private String mKey = null;
     private String mValue = null;
 
@@ -51,6 +52,8 @@ public class VCFHeaderLine implements Comparable {
      * @param value   the value for this header line
      */
     public VCFHeaderLine(String key, String value) {
+        if ( key == null )
+            throw new IllegalArgumentException("VCFHeaderLine: key cannot be null: key = " + key);
         mKey = key;
         mValue = value;
     }
@@ -64,16 +67,6 @@ public class VCFHeaderLine implements Comparable {
         return mKey;
     }
 
-    /**
-     * Set the key
-     *
-     * @param key     the key for this header line
-     */
-    public void setKey(String key) {
-        mKey = key;
-        stringRep = null;
-    }
-
     /**
      * Get the value
      *
@@ -83,22 +76,15 @@ public class VCFHeaderLine implements Comparable {
         return mValue;
     }
 
-    /**
-     * Set the value
-     *
-     * @param value     the value for this header line
-     */
-    public void setValue(String value) {
-        mValue = value;
-        stringRep = null;
-    }
-
     public String toString() {
-        if ( stringRep == null )
+        return toStringEncoding();
-            stringRep = toStringEncoding();
-        return stringRep;
     }
 
+    /**
+     * Should be overloaded in sub classes to do subclass specific
+     *
+     * @return
+     */
     protected String toStringEncoding() {
         return mKey + "=" + mValue;
     }

java/src/org/broad/tribble/vcf/VCFInfoHeaderLine.java

@@ -9,11 +9,6 @@ package org.broad.tribble.vcf;
  *         A class representing a key=value entry for INFO fields in the VCF header
  */
 public class VCFInfoHeaderLine extends VCFCompoundHeaderLine {
-
-    public VCFInfoHeaderLine(String name, int count, VCFHeaderLineType type, String description, VCFHeaderVersion version) {
-        super(name, count, type, description, SupportedHeaderLineType.INFO, version);
-    }
-
     public VCFInfoHeaderLine(String name, int count, VCFHeaderLineType type, String description) {
         super(name, count, type, description, SupportedHeaderLineType.INFO);
     }