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[Treebase-guts] SF.net SVN: treebase:[79] trunk/treebase-core/src/main/java/org/cipres/ treebase/TreebaseIDString.java
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From: <rv...@us...> - 2009-06-23 11:51:02
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Revision: 79
http://treebase.svn.sourceforge.net/treebase/?rev=79&view=rev
Author: rvos
Date: 2009-06-23 11:05:11 +0000 (Tue, 23 Jun 2009)
Log Message:
-----------
Adding many new types for prefix mappings, adding usage of NamespacedGUID
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/TreebaseIDString.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/TreebaseIDString.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/TreebaseIDString.java 2009-06-23 11:03:39 UTC (rev 78)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/TreebaseIDString.java 2009-06-23 11:05:11 UTC (rev 79)
@@ -4,41 +4,56 @@
import java.util.Map;
import org.cipres.treebase.domain.TBPersistable;
+import org.cipres.treebase.domain.matrix.DiscreteCharState;
+import org.cipres.treebase.domain.matrix.DiscreteMatrixElement;
import org.cipres.treebase.domain.matrix.Matrix;
+import org.cipres.treebase.domain.matrix.PhyloChar;
import org.cipres.treebase.domain.study.Analysis;
import org.cipres.treebase.domain.study.AnalysisStep;
import org.cipres.treebase.domain.study.AnalyzedData;
import org.cipres.treebase.domain.study.Study;
import org.cipres.treebase.domain.taxon.Taxon;
import org.cipres.treebase.domain.taxon.TaxonLabel;
+import org.cipres.treebase.domain.taxon.TaxonLabelSet;
import org.cipres.treebase.domain.taxon.TaxonVariant;
import org.cipres.treebase.domain.tree.PhyloTree;
import org.cipres.treebase.domain.tree.PhyloTreeNode;
+import org.cipres.treebase.domain.tree.TreeBlock;
+import org.nexml.model.Annotatable;
public class TreebaseIDString {
public class MalformedTreebaseIDString extends Exception {
+ private static final long serialVersionUID = 1L;
public MalformedTreebaseIDString() {
super();
}
-
public MalformedTreebaseIDString(String message) {
super(message);
}
}
- private static final Map<Class,String> prefixFor = initializePrefixForMap();
- private static final Map<String,Class> classFor = initializeClassForMap();
+
+ private static final Map<Class<?>,String> prefixFor = initializePrefixForMap();
+ private static final Map<String,Class<?>> classFor = initializeClassForMap();
+ private String mTypePrefix;
+ private Long mId;
+
// These are the canonical prefixes
- private static Map<Class, String> initializePrefixForMap() {
- Map<Class, String> val = new HashMap<Class, String> ();
+ private static Map<Class<?>, String> initializePrefixForMap() {
+ Map<Class<?>, String> val = new HashMap<Class<?>, String> ();
val.put(Study.class, "S");
val.put(Matrix.class, "M");
+ val.put(PhyloChar.class, "C");
+ val.put(DiscreteCharState.class, "Dcs");
+ val.put(DiscreteMatrixElement.class, "Dme");
val.put(PhyloTree.class, "Tr");
val.put(PhyloTreeNode.class, "Tn");
+ val.put(TreeBlock.class, "Tb");
val.put(Taxon.class, "Tx");
val.put(TaxonLabel.class, "Tl");
+ val.put(TaxonLabelSet.class, "Tls");
val.put(TaxonVariant.class, "Tv");
val.put(Analysis.class, "A");
val.put(AnalysisStep.class, "As");
@@ -50,31 +65,28 @@
// and also some aliases.
// For example, the application will always use "Tr1000" as the ID string for PhyloTree 1000
// but it will accept "T1000" as an alias.
- private static Map<String, Class> initializeClassForMap() {
- Map<String, Class> val = new HashMap<String, Class> ();
- for (Map.Entry<Class, String> e : prefixFor.entrySet()) {
+ private static Map<String, Class<?>> initializeClassForMap() {
+ Map<String, Class<?>> val = new HashMap<String, Class<?>> ();
+ for (Map.Entry<Class<?>, String> e : prefixFor.entrySet()) {
val.put(e.getValue(), e.getKey());
}
val.put("T", PhyloTree.class);
return val;
}
- String typePrefix;
- Long id;
-
public TreebaseIDString(String typePrefix, Long id) {
- this.typePrefix = typePrefix;
- this.id = id;
+ mTypePrefix = typePrefix;
+ mId = id;
}
- public TreebaseIDString(Class typeClass, Long id) {
- this.typePrefix = getPrefixForClass(typeClass);
- this.id = id;
+ public TreebaseIDString(Class<?> typeClass, Long id) {
+ mTypePrefix = getPrefixForClass(typeClass);
+ mId = id;
}
public TreebaseIDString(TBPersistable tbObj) {
- this.typePrefix = getPrefixForClass(tbObj.getClass());
- this.id = tbObj.getId();
+ mTypePrefix = getPrefixForClass(tbObj.getClass());
+ mId = tbObj.getId();
}
/**
@@ -97,43 +109,44 @@
* @param mustMatch - if set, an exception is thrown if the type prefix in ids does not match the defaultClass
* @throws MalformedTreebaseIDString
*/
- public TreebaseIDString(String ids, Class defaultClass, boolean mustMatch) throws MalformedTreebaseIDString {
+ public TreebaseIDString(String ids, Class<?> defaultClass, boolean mustMatch) throws MalformedTreebaseIDString {
try {
- this.parseWithoutSemanticChecks(ids);
+ parseWithoutSemanticChecks(ids);
} catch (NumberFormatException e) {
throw new MalformedTreebaseIDString(ids);
}
- if (this.getId() == null) throw new MalformedTreebaseIDString(ids);
+ if (getId() == null) throw new MalformedTreebaseIDString(ids);
// If there was no prefix, try to infer one
- if (this.getTypePrefix() == null || this.getTypePrefix().equals("")) {
- this.typePrefix = getPrefixForClass(defaultClass);
- if (this.getTypePrefix() == null)
+ if (getTypePrefix() == null || getTypePrefix().equals("")) {
+ mTypePrefix = getPrefixForClass(defaultClass);
+ if (getTypePrefix() == null)
throw new MalformedTreebaseIDString(ids);
}
else {
// also validate as usual
- this.validateTypePrefix();
+ validateTypePrefix();
// If requested, make sure the prefix matches the requested class
- if (mustMatch)
- if (getClassForPrefix(this.getTypePrefix()) != defaultClass)
+ if ( mustMatch ) {
+ if (getClassForPrefix(getTypePrefix()) != defaultClass) {
throw new MalformedTreebaseIDString(ids + " has wrong prefix; should be " + getPrefixForClass(defaultClass));
+ }
+ }
}
}
- public TreebaseIDString(String string, Class class1) throws MalformedTreebaseIDString {
+ public TreebaseIDString(String string, Class<?> class1) throws MalformedTreebaseIDString {
this(string, class1, false);
}
public TreebaseIDString(String ids) throws MalformedTreebaseIDString {
try {
- this.parseWithoutSemanticChecks(ids);
+ parseWithoutSemanticChecks(ids);
} catch (NumberFormatException e) {
throw new MalformedTreebaseIDString(ids);
- }
-
- this.validateTypePrefix();
+ }
+ validateTypePrefix();
}
@@ -177,8 +190,8 @@
if (i < ids.length()) throw new MalformedTreebaseIDString("..." + ids.substring(i));
- this.id = Long.parseLong(digits.toString());
- this.typePrefix = prefix.toString();
+ mId = Long.parseLong(digits.toString());
+ mTypePrefix = prefix.toString();
}
String getIDString() {
@@ -217,7 +230,7 @@
* @param prefix
* @return
*/
- public static Class getClassForPrefix(String prefix) {
+ public static Class<?> getClassForPrefix(String prefix) {
return classFor.get(prefix);
}
@@ -230,7 +243,7 @@
* @param cl - the class
* @return
*/
- public static String getPrefixForClass(Class cl) {
+ public static String getPrefixForClass(Class<?> cl) {
return prefixFor.get(cl);
}
@@ -279,19 +292,41 @@
* @param idString
* @return
*/
- public static Class getClassForIDString(String idString) {
+ public static Class<?> getClassForIDString(String idString) {
return getClassForPrefix(getPrefixOf(idString));
}
public String getTypePrefix() {
- return typePrefix;
+ return mTypePrefix;
}
public Long getId() {
- return id;
+ return mId;
}
- public Class getTBClass() {
+ public Class<?> getTBClass() {
return getClassForPrefix(getTypePrefix());
}
+
+ /**
+ * This creates a GUID of the form TB2:${mTypePrefix}${mId}, which is the
+ * minimal recommendation for, for example, dc:identifier annotations.
+ * Additional blogging by Rod Page and others about this suggests there
+ * should be a delimiter between mTypePrefix and mId so that we'd end up
+ * with id's that look like TB2:Tr:2131, which could then be mapped onto
+ * purls. But doing that would break our backward compatibility with older
+ * records, files, etc.
+ *
+ * @return
+ */
+ public NamespacedGUID getNamespacedGUID() {
+ StringBuilder sb = new StringBuilder();
+ sb
+ .append(NamespacedGUID.getDefaultGUIDPrefix())
+ .append(getTypePrefix())
+ .append(getId());
+ return new NamespacedGUID(sb.toString());
+ }
+
+
}
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