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treebase-guts
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From: <rv...@us...> - 2009-06-23 12:49:16
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Revision: 76
http://treebase.svn.sourceforge.net/treebase/?rev=76&view=rev
Author: rvos
Date: 2009-06-23 10:57:15 +0000 (Tue, 23 Jun 2009)
Log Message:
-----------
Fix: now no longer returns PhyloTreenull as a default title. Instead, if getId() returns a value, return a TreebaseIDString, otherwise return null.
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTree.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTree.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTree.java 2009-06-23 10:56:13 UTC (rev 75)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTree.java 2009-06-23 10:57:15 UTC (rev 76)
@@ -46,6 +46,7 @@
import mesquite.lib.MesquiteDouble;
import mesquite.lib.StringUtil;
+import org.cipres.treebase.TreebaseIDString;
import org.cipres.treebase.TreebaseUtil;
import org.cipres.treebase.domain.AbstractPersistedObject;
import org.cipres.treebase.domain.TBPersistable;
@@ -224,8 +225,11 @@
if ( ! TreebaseUtil.isEmpty(mTitle) ) {
return mTitle;
}
+ else if ( null != getId() ){
+ return TreebaseIDString.getIDString(this);
+ }
else {
- return "PhyloTree" + getId();
+ return null;
}
}
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From: <rv...@us...> - 2010-03-15 01:16:49
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Revision: 581
http://treebase.svn.sourceforge.net/treebase/?rev=581&view=rev
Author: rvos
Date: 2010-03-15 01:16:43 +0000 (Mon, 15 Mar 2010)
Log Message:
-----------
Added getAnnotations() for nexml and rdf serialization.
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTree.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTree.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTree.java 2010-03-15 01:15:19 UTC (rev 580)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTree.java 2010-03-15 01:16:43 UTC (rev 581)
@@ -4,6 +4,7 @@
import java.util.Collections;
import java.util.HashSet;
import java.util.Iterator;
+import java.util.List;
import java.util.Set;
import javax.persistence.AttributeOverride;
@@ -25,9 +26,11 @@
import mesquite.lib.MesquiteDouble;
import mesquite.lib.StringUtil;
+import org.cipres.treebase.Constants;
import org.cipres.treebase.TreebaseIDString;
import org.cipres.treebase.TreebaseUtil;
import org.cipres.treebase.domain.AbstractPersistedObject;
+import org.cipres.treebase.domain.Annotation;
import org.cipres.treebase.domain.TBPersistable;
import org.cipres.treebase.domain.study.Study;
import org.cipres.treebase.domain.taxon.TaxonLabel;
@@ -227,6 +230,7 @@
*
* @return String
*/
+ @Override
@Column(name = "Label", length = TBPersistable.COLUMN_LENGTH_STRING)
public String getLabel() {
return mLabel;
@@ -778,4 +782,26 @@
setRootNode(null);
setNewickString(null);
}
+
+ @Transient
+ public List<Annotation> getAnnotations() {
+ List<Annotation> annotations = super.getAnnotations();
+ if ( null != getId() ) {
+ annotations.add(new Annotation(Constants.TBTermsURI, "tb:identifier.tree", getId()));
+ }
+ if ( null != getKindDescription() ) {
+ annotations.add(new Annotation(Constants.TBTermsURI, "tb:kind.tree", getKindDescription()));
+ }
+ if ( null != getTypeDescription() ) {
+ annotations.add(new Annotation(Constants.TBTermsURI, "tb:type.tree", getTypeDescription()));
+ }
+ if ( null != getQualityDescription() ) {
+ annotations.add(new Annotation(Constants.TBTermsURI, "tb:quality.tree", getQualityDescription()));
+ }
+ if ( null != getnTax() ) {
+ annotations.add(new Annotation(Constants.TBTermsURI, "tb:ntax.tree", getnTax()));
+ }
+ return annotations;
+ }
+
}
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From: <rv...@us...> - 2010-03-16 17:00:56
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Revision: 609
http://treebase.svn.sourceforge.net/treebase/?rev=609&view=rev
Author: rvos
Date: 2010-03-16 17:00:50 +0000 (Tue, 16 Mar 2010)
Log Message:
-----------
Implemented getContext, which returns the containing study. Wrapped annotation generation inside a try {} block (I was getting some lazy initialization exceptions), changed the fetch mode to join, to prevent lazy initialization exceptions.
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTree.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTree.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTree.java 2010-03-16 16:58:15 UTC (rev 608)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTree.java 2010-03-16 17:00:50 UTC (rev 609)
@@ -37,6 +37,8 @@
import org.hibernate.annotations.BatchSize;
import org.hibernate.annotations.Cache;
import org.hibernate.annotations.CacheConcurrencyStrategy;
+import org.hibernate.annotations.Fetch;
+import org.hibernate.annotations.FetchMode;
import org.hibernate.annotations.NamedNativeQuery;
/**
@@ -284,6 +286,7 @@
*/
@ManyToOne(cascade = {CascadeType.PERSIST, CascadeType.MERGE}, fetch = FetchType.LAZY)
@JoinColumn(name = "TREEQUALITY_ID")
+ @Fetch(FetchMode.JOIN)
public TreeQuality getTreeQuality() {
return mTreeQuality;
}
@@ -320,6 +323,7 @@
*/
@ManyToOne(fetch = FetchType.LAZY)
@JoinColumn(name = "TREEKIND_ID")
+ @Fetch(FetchMode.JOIN)
public TreeKind getTreeKind() {
return mTreeKind;
}
@@ -338,6 +342,7 @@
*/
@ManyToOne(cascade = {CascadeType.PERSIST, CascadeType.MERGE}, fetch = FetchType.LAZY)
@JoinColumn(name = "TREETYPE_ID")
+ @Fetch(FetchMode.JOIN)
public TreeType getTreeType() {
return mTreeType;
}
@@ -786,22 +791,29 @@
@Transient
public List<Annotation> getAnnotations() {
List<Annotation> annotations = super.getAnnotations();
- if ( null != getId() ) {
- annotations.add(new Annotation(Constants.TBTermsURI, "tb:identifier.tree", getId()));
+ try {
+ if ( null != getKindDescription() ) {
+ annotations.add(new Annotation(Constants.TBTermsURI, "tb:kind.tree", getKindDescription()));
+ }
+ if ( null != getTypeDescription() ) {
+ annotations.add(new Annotation(Constants.TBTermsURI, "tb:type.tree", getTypeDescription()));
+ }
+ if ( null != getQualityDescription() ) {
+ annotations.add(new Annotation(Constants.TBTermsURI, "tb:quality.tree", getQualityDescription()));
+ }
+ if ( null != getnTax() ) {
+ annotations.add(new Annotation(Constants.TBTermsURI, "tb:ntax.tree", getnTax()));
+ }
+ } catch ( Exception e ) {
+ e.printStackTrace();
}
- if ( null != getKindDescription() ) {
- annotations.add(new Annotation(Constants.TBTermsURI, "tb:kind.tree", getKindDescription()));
- }
- if ( null != getTypeDescription() ) {
- annotations.add(new Annotation(Constants.TBTermsURI, "tb:type.tree", getTypeDescription()));
- }
- if ( null != getQualityDescription() ) {
- annotations.add(new Annotation(Constants.TBTermsURI, "tb:quality.tree", getQualityDescription()));
- }
- if ( null != getnTax() ) {
- annotations.add(new Annotation(Constants.TBTermsURI, "tb:ntax.tree", getnTax()));
- }
return annotations;
}
+
+ @Override
+ @Transient
+ public Study getContext() {
+ return getStudy();
+ }
}
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From: <hs...@us...> - 2011-06-10 19:41:41
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Revision: 909
http://treebase.svn.sourceforge.net/treebase/?rev=909&view=rev
Author: hshyket
Date: 2011-06-10 19:41:35 +0000 (Fri, 10 Jun 2011)
Log Message:
-----------
Fixing issue with semicolon not being at the end of the tree in a nexus file.
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTree.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTree.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTree.java 2011-06-10 16:47:32 UTC (rev 908)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTree.java 2011-06-10 19:41:35 UTC (rev 909)
@@ -569,6 +569,14 @@
}
}
+
+ //check to see if the NewickString has a semicolon in it
+ String newWick = getNewickString();
+
+ if (newWick.indexOf(';') == -1) {
+ newWick.concat(";");
+ }
+
pBuilder.append(getNewickString()).append("\n");
pBuilder.append("[! TreeBASE tree URI: ").append(getPhyloWSPath().getPurl()).append("]\n");
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From: <hs...@us...> - 2011-06-10 20:41:48
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Revision: 910
http://treebase.svn.sourceforge.net/treebase/?rev=910&view=rev
Author: hshyket
Date: 2011-06-10 20:41:41 +0000 (Fri, 10 Jun 2011)
Log Message:
-----------
Fixing error with last commit.
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTree.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTree.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTree.java 2011-06-10 19:41:35 UTC (rev 909)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTree.java 2011-06-10 20:41:41 UTC (rev 910)
@@ -577,7 +577,7 @@
newWick.concat(";");
}
- pBuilder.append(getNewickString()).append("\n");
+ pBuilder.append(newWick).append("\n");
pBuilder.append("[! TreeBASE tree URI: ").append(getPhyloWSPath().getPurl()).append("]\n");
pBuilder.append("\n\nEND;\n");
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From: <hs...@us...> - 2011-06-14 19:14:44
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Revision: 917
http://treebase.svn.sourceforge.net/treebase/?rev=917&view=rev
Author: hshyket
Date: 2011-06-14 19:14:38 +0000 (Tue, 14 Jun 2011)
Log Message:
-----------
Fixing newWick string
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTree.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTree.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTree.java 2011-06-14 13:06:13 UTC (rev 916)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTree.java 2011-06-14 19:14:38 UTC (rev 917)
@@ -574,10 +574,11 @@
String newWick = getNewickString();
if (newWick.indexOf(';') == -1) {
- newWick.concat(";");
+ newWick = newWick + ";";
}
pBuilder.append(newWick).append("\n");
+
pBuilder.append("[! TreeBASE tree URI: ").append(getPhyloWSPath().getPurl()).append("]\n");
pBuilder.append("\n\nEND;\n");
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