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[Treebase-guts] SF.net SVN: treebase:[659] trunk
|
From: <yo...@us...> - 2010-03-29 19:35:09
|
Revision: 659
http://treebase.svn.sourceforge.net/treebase/?rev=659&view=rev
Author: youjun
Date: 2010-03-29 19:34:59 +0000 (Mon, 29 Mar 2010)
Log Message:
-----------
fix delete matrix, fix limitedphylowidget zooming tool
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/MatrixJDBC.java
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/matrix/MatrixDAO.java
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/taxon/TaxonLabelDAO.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/CharacterMatrix.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/MatrixHome.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabel.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabelHome.java
trunk/treebase-core/src/main/resources/applicationContext-dao.xml
trunk/treebase-phylowidget/build.properties
trunk/treebase-web/src/main/resources/ApplicationResources.properties
trunk/treebase-web/src/main/webapp/test/phylowidget/PhyloWidget.jar
Added Paths:
-----------
trunk/treebase-phylowidget/data/menus/limited-menus.xml
Removed Paths:
-------------
trunk/treebase-phylowidget/data/menus/nondb-menus.xml
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/MatrixJDBC.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/MatrixJDBC.java 2010-03-27 01:02:51 UTC (rev 658)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/MatrixJDBC.java 2010-03-29 19:34:59 UTC (rev 659)
@@ -124,6 +124,28 @@
}
/**
+ * Delete all rows and associated objects using direct SQL.
+ *
+ * @param pMatrix
+ * @param pSession
+ */
+ public static void deleteMatrixRowSQL(CharacterMatrix pMatrix, Session pSession) {
+ // delete all matrix rows by direct JDBC:
+ // * delete all row segments
+ // * delete all rows
+
+ String query = "DELETE FROM ROWSEGMENT WHERE MATRIXROW_ID in (select row.MATRIXROW_ID from MATRIXROW row where row.MATRIX_ID = :matrixID)";
+ Query q = pSession.createSQLQuery(query);
+ q.setParameter("matrixID", pMatrix.getId());
+ q.executeUpdate();
+
+ query = "DELETE FROM MATRIXROW WHERE MATRIX_ID = :matrixID";
+ q = pSession.createSQLQuery(query);
+ q.setParameter("matrixID", pMatrix.getId());
+ q.executeUpdate();
+
+ }
+ /**
* Delete all elements and associated objects in a matrix using direct SQL.
*
* @param pTree
@@ -153,8 +175,8 @@
q.setParameter("matrixID", pMatrix.getId());
q.executeUpdate();
- query = "delete from matrixelement where matrixelement_id IN "
- + "(select m.matrixelement_id from matrixelement m, MATRIXCOLUMN c where m.MATRIXCOLUMN_ID = c.MATRIXCOLUMN_ID and c.MATRIX_ID = :matrixID)";
+ query = "DELETE FROM matrixelement WHERE matrixcolumn_id IN"
+ + "(SELECT c.matrixcolumn_id FROM matrixcolumn c WHERE c.matrix_id = :matrixID)";
q = pSession.createSQLQuery(query);
q.setParameter("matrixID", pMatrix.getId());
q.executeUpdate();
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/dao/matrix/MatrixDAO.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/dao/matrix/MatrixDAO.java 2010-03-27 01:02:51 UTC (rev 658)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/dao/matrix/MatrixDAO.java 2010-03-29 19:34:59 UTC (rev 659)
@@ -28,6 +28,9 @@
import org.cipres.treebase.domain.study.Study;
import org.cipres.treebase.domain.study.Submission;
import org.cipres.treebase.domain.study.SubmissionHome;
+import org.cipres.treebase.domain.taxon.TaxonLabel;
+import org.cipres.treebase.domain.taxon.TaxonLabelHome;
+import org.cipres.treebase.domain.taxon.TaxonLabelSet;
import org.apache.log4j.Logger;
import org.hibernate.Criteria;
@@ -50,7 +53,8 @@
private MatrixRowHome mMatrixRowHome;
private SubmissionHome mSubmissionHome;
private AnalyzedDataHome mAnalyzedDataHome;
-
+ private TaxonLabelHome mTaxonLabelHome;
+
/**
* Constructor.
*/
@@ -107,6 +111,25 @@
}
/**
+ * set the TaxonLabelHome field.
+ */
+ public void setTaxonLabelHome(TaxonLabelHome pNewTaxonLabelHome) {
+ mTaxonLabelHome = pNewTaxonLabelHome;
+ }
+
+ /**
+ * Return the TaxonLabelHome field.
+ *
+ *
+ * @return TaxonLabelHome mTaxonLabelHome
+ */
+ private TaxonLabelHome getTaxonLabelHome() {
+ return mTaxonLabelHome;
+ }
+
+
+
+ /**
* Return the SubmissionHome field.
*
* @return SubmissionHome mSubmissionHome
@@ -138,6 +161,35 @@
/**
*
+ * @see org.cipres.treebase.domain.matrix.MatrixHome#cascadeDelete(org.cipres.treebase.domain.matrix.CharacterMatrix)
+ */
+ public void cascadeDelete(CharacterMatrix pMatrix) {
+
+ // bi-directional relationships:
+ // * delete submission-> matrix
+ // * delete analyzedData -> matrix
+ Submission sub = getSubmissionHome().findByMatrix(pMatrix);
+ if (sub != null) {
+ sub.removeMatrix(pMatrix);
+ }
+
+ Collection<AnalyzedData> dataLink = getAnalyzedDataHome().findByMatrix(pMatrix);
+ for (AnalyzedData data : dataLink) {
+ data.getAnalysisStep().removeAnalyzedData(data);
+ }
+
+ TaxonLabelSet tSet = pMatrix.getTaxa();
+ List<TaxonLabel> tList = pMatrix.getAllTaxonLabels();
+
+ getHibernateTemplate().delete(pMatrix);
+
+ getTaxonLabelHome().clean(tSet);
+ getTaxonLabelHome().clean(tList);
+
+ }
+
+ /**
+ *
* @see org.cipres.treebase.domain.matrix.MatrixHome#delete(org.cipres.treebase.domain.matrix.Matrix)
*/
public void delete(Matrix pMatrix) {
@@ -145,21 +197,8 @@
// Use double dispatch.
pMatrix.cascadeDelete(this);
-
- // bi-directional relationships:
- // * delete submission-> matrix
- // * delete analyzedData -> matrix
- Submission sub = getSubmissionHome().findByMatrix(pMatrix);
- if (sub != null) {
- sub.removeMatrix(pMatrix);
- }
-
- Collection<AnalyzedData> dataLink = getAnalyzedDataHome().findByMatrix(pMatrix);
- for (AnalyzedData data : dataLink) {
- data.getAnalysisStep().removeAnalyzedData(data);
- }
-
- getHibernateTemplate().delete(pMatrix);
+
+
}
}
@@ -184,8 +223,17 @@
getMatrixRowHome().deleteRows(pRows);
}
+
/**
*
+ * @see org.cipres.treebase.domain.matrix.MatrixHome#cascadeDeleteRows(java.util.Collection)
+ */
+ public void cascadeDeleteRows(CharacterMatrix pMatrix) {
+ MatrixJDBC.deleteMatrixRowSQL(pMatrix,getSession());
+ }
+
+ /**
+ *
* @see org.cipres.treebase.domain.matrix.MatrixHome#cascadeDeleteAncStateSet(java.util.Set)
*/
public void cascadeDeleteAncStateSet(Set<AncStateSet> pAncStateSets) {
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/dao/taxon/TaxonLabelDAO.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/dao/taxon/TaxonLabelDAO.java 2010-03-27 01:02:51 UTC (rev 658)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/dao/taxon/TaxonLabelDAO.java 2010-03-29 19:34:59 UTC (rev 659)
@@ -466,12 +466,12 @@
Query q = getSession()
.createQuery("select count(*) from TreeBlock tb where tb.taxonLabelSet = :ts");
q.setParameter("ts", tSet);
- int count=((Integer)q.iterate().next()).intValue();
+ int count=((Long)q.iterate().next()).intValue();
q = getSession()
.createQuery("select count(*) from Matrix m where m.taxa = :ts");
q.setParameter("ts", tSet);
- count += ((Integer)q.iterate().next()).intValue();
+ count += ((Long)q.iterate().next()).intValue();
if(count==0)deletePersist(tSet);
}
@@ -482,12 +482,12 @@
Query q = getSession()
.createQuery("select count(*) from PhyloTreeNode pn where pn.taxonLabel = :tl");
q.setParameter("tl", tl);
- int count=((Integer)q.iterate().next()).intValue();
+ int count=((Long)q.iterate().next()).intValue();
q = getSession()
.createQuery("select count(*) from MatrixRow mr where mr.taxonLabel = :tl");
q.setParameter("tl", tl);
- count += ((Integer)q.iterate().next()).intValue();
+ count += ((Long)q.iterate().next()).intValue();
if(count==0)deletePersist(tl);
}
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/CharacterMatrix.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/CharacterMatrix.java 2010-03-27 01:02:51 UTC (rev 658)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/CharacterMatrix.java 2010-03-29 19:34:59 UTC (rev 659)
@@ -83,7 +83,7 @@
*
* @return CodonPositionSet
*/
- @OneToOne(cascade = {CascadeType.PERSIST, CascadeType.MERGE})
+ @OneToOne(cascade = {CascadeType.ALL})
@JoinColumn(name = "CODONPOSITIONSET_ID", nullable = true)
public CodonPositionSet getDefaultCodonPosSet() {
return mDefaultCodonPosSet;
@@ -111,7 +111,7 @@
*
* @return CharWeightSet
*/
- @OneToOne(cascade = {CascadeType.PERSIST, CascadeType.MERGE})
+ @OneToOne(cascade = {CascadeType.ALL})
@JoinColumn(name = "CHARWEIGHTSET_ID", nullable = true)
public CharWeightSet getDefaultWeightSet() {
return mDefaultWeightSet;
@@ -139,7 +139,7 @@
*
* @return ExcludedCharSet
*/
- @OneToOne(cascade = {CascadeType.PERSIST, CascadeType.MERGE})
+ @OneToOne(cascade = {CascadeType.ALL})
@JoinColumn(name = "CHARSET_ID", nullable = true)
public ExcludedCharSet getDefaultExcludedSet() {
return mDefaultExcludedSet;
@@ -167,7 +167,7 @@
*
* @return TypeSet mDefaultTypeSet
*/
- @OneToOne(cascade = {CascadeType.PERSIST, CascadeType.MERGE})
+ @OneToOne(cascade = {CascadeType.ALL})
@JoinColumn(name = "TYPESET_ID", nullable = true)
public TypeSet getDefaultTypeSet() {
return mDefaultTypeSet;
@@ -332,7 +332,7 @@
*
* @return AncStateSet
*/
- @OneToOne(cascade = {CascadeType.PERSIST, CascadeType.MERGE})
+ @OneToOne(cascade = {CascadeType.ALL})
@JoinColumn(name = "ANCSTATESET_ID", nullable = true)
public AncStateSet getDefaultAncSet() {
return mDefaultAncSet;
@@ -358,7 +358,7 @@
//@OneToMany(cascade = CascadeType.ALL)
// no cascade merge since we do not modify a column ?? Need test.
//@OneToMany(cascade = {CascadeType.PERSIST, CascadeType.REMOVE})
- @OneToMany
+ @OneToMany(cascade = {CascadeType.ALL})
@JoinColumn(name = "MATRIX_ID")
@IndexColumn(name = "COLUMN_ORDER")
@Cache(usage = CacheConcurrencyStrategy.NONSTRICT_READ_WRITE, region = "matrixCache")
@@ -445,10 +445,10 @@
// private Set<CodonPositionSet> mCodonPosSets;
// private Set<GeneticCodeSet> mCodeSets;
// private Set<TypeSet> mTypeSets;
-
- pMatrixHome.cascadeDeleteElements(this);
- pMatrixHome.cascadeDeleteRows(getRows());
- pMatrixHome.cascadeDeleteColumns(this);
+ pMatrixHome.cascadeDelete(this);
+ //pMatrixHome.cascadeDeleteElements(this);
+ //pMatrixHome.cascadeDeleteRows(this);
+ //pMatrixHome.cascadeDeleteColumns(this);
// pMatrixHome.cascadeDeleteAncStateSet(getAncStateSets());
// pMatrixHome.cascadeDeleteCharWeightSet(getWeightSets());
@@ -508,7 +508,7 @@
// the one side has to be the owner side, cannot use "mappedby"
// also need to duplicate specify the JoinColumn here.
// @OneToMany(mappedBy = "matrix", cascade = CascadeType.ALL)
- @OneToMany(cascade = {CascadeType.MERGE, CascadeType.PERSIST})
+ @OneToMany(cascade = {CascadeType.ALL})
@JoinColumn(name = "MATRIX_ID")
@IndexColumn(name = "ROW_ORDER")
@Cache(usage = CacheConcurrencyStrategy.NONSTRICT_READ_WRITE, region = "matrixCache")
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/MatrixHome.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/MatrixHome.java 2010-03-27 01:02:51 UTC (rev 658)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/MatrixHome.java 2010-03-29 19:34:59 UTC (rev 659)
@@ -55,14 +55,14 @@
* @param pMatrix
*/
void cascadeDeleteColumns(CharacterMatrix pMatrix);
-
+ void cascadeDelete(CharacterMatrix pMatrix);
/**
* Delete a collection of matrix rows.
*
* @param pRows
*/
void cascadeDeleteRows(Collection<MatrixRow> pRows);
-
+ void cascadeDeleteRows(CharacterMatrix pMatrix);
/**
* Delete a collection of ancestral state sets.
*
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabel.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabel.java 2010-03-27 01:02:51 UTC (rev 658)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabel.java 2010-03-29 19:34:59 UTC (rev 659)
@@ -10,6 +10,8 @@
import javax.persistence.Entity;
import javax.persistence.FetchType;
import javax.persistence.JoinColumn;
+import javax.persistence.JoinTable;
+import javax.persistence.ManyToMany;
import javax.persistence.ManyToOne;
import javax.persistence.Table;
import javax.persistence.Transient;
@@ -54,6 +56,7 @@
private TaxonVariant mTaxonVariant;
private Study mStudy;
+ private Submission mSubmission;
/**
* Constructor.
@@ -173,14 +176,28 @@
*
* @return the submission
* @author mjd 20080929
+ * modified by Youjun
*/
- @Transient
+ @ManyToOne(cascade = {CascadeType.MERGE, CascadeType.PERSIST, CascadeType.REFRESH})
+ @JoinTable(name = "sub_taxonlabel",
+ joinColumns = @JoinColumn(name = "taxonlabel_id"),
+ inverseJoinColumns = @JoinColumn(name="submission_id")
+
+ )
public Submission getSubmission() {
- Study s = getStudy();
- return s == null ? null : s.getSubmission();
+
+ return mSubmission;
}
/**
+ * Set the Submission field.
+ */
+ public void setSubmission(Submission pNewSubmission) {
+ mSubmission = pNewSubmission;
+ }
+
+
+ /**
* Return the taxon name if it available.
*/
@Transient
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabelHome.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabelHome.java 2010-03-27 01:02:51 UTC (rev 658)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabelHome.java 2010-03-29 19:34:59 UTC (rev 659)
@@ -2,6 +2,7 @@
package org.cipres.treebase.domain.taxon;
import java.util.Collection;
+import java.util.List;
import java.util.Set;
import org.cipres.treebase.domain.DomainHome;
@@ -229,4 +230,15 @@
* @return All taxonlabelsets of which this taxonlabel is a member
*/
Set<TaxonLabelSet> findTaxonLabelSets(TaxonLabel tl);
+
+ /**
+ * clean orphan record @ TaxonLabelSet
+ */
+ public void clean(TaxonLabelSet tSet);
+
+ /**
+ * clean orphan record @ TaxonLabel
+ */
+ public void clean(List<TaxonLabel> tList);
+
}
Modified: trunk/treebase-core/src/main/resources/applicationContext-dao.xml
===================================================================
--- trunk/treebase-core/src/main/resources/applicationContext-dao.xml 2010-03-27 01:02:51 UTC (rev 658)
+++ trunk/treebase-core/src/main/resources/applicationContext-dao.xml 2010-03-29 19:34:59 UTC (rev 659)
@@ -173,6 +173,7 @@
<property name="matrixRowHome" ref="matrixRowHome" />
<property name="submissionHome" ref="submissionHome" />
<property name="analyzedDataHome" ref="analyzedDataHome" />
+ <property name="taxonLabelHome" ref="taxonLabelHome" />
</bean>
</property>
</bean>
Modified: trunk/treebase-phylowidget/build.properties
===================================================================
--- trunk/treebase-phylowidget/build.properties 2010-03-27 01:02:51 UTC (rev 658)
+++ trunk/treebase-phylowidget/build.properties 2010-03-29 19:34:59 UTC (rev 659)
@@ -49,7 +49,7 @@
# Whether or not to try and sign the jar.
signjar = true
# Whether or not to generate a new key. Set the value to true if it is the first time to run ant build in this machine.
-signjar.genkey = false
+signjar.genkey = true
# Your keystore alias and password.
signjar.alias = phylowidget
signjar.storepass = birdman
Added: trunk/treebase-phylowidget/data/menus/limited-menus.xml
===================================================================
--- trunk/treebase-phylowidget/data/menus/limited-menus.xml (rev 0)
+++ trunk/treebase-phylowidget/data/menus/limited-menus.xml 2010-03-29 19:34:59 UTC (rev 659)
@@ -0,0 +1,81 @@
+<menuset name="PhyloWidget Menus">
+ <menu type="Toolbar" fontsize="11" x="2" y="2">
+ <item name="File">
+ <!--item name="New Tree" action="treeNew" shortcut="control-n"/-->
+ <!--item name="Load Tree..." action="treeLoad"/-->
+ <item name="Save Tree..." action="treeSave"/>
+ <!--item name="Save Tree To Database" action="treeSaveToDB"/-->
+ <item name="Export Image">
+ <item name="Large (1600x1200)" action="fileOutputBig"/>
+ <item name="Small (640 x 480)" action="fileOutputSmall"/>
+ <item name="PDF" action="fileOutputPDF"/>
+ </item>
+ </item>
+ <item name="View">
+ <item name="Zoom to Full" action="viewZoomToFull" shortcut="control-F"/>
+ <item name="Renderer Type">
+ <item name="Rectangular" action="viewRectangular" shortcut="control-1"/>
+ <item name="Diagonal" action="viewDiagonal" shortcut="control-2"/>
+ <item name="Circular" action="viewCircular" shortcut="control-3"/>
+ </item>
+ <item name="Show/Hide">
+ <item name="Branch Lengths" type="CheckBox" property="showBranchLengths" value="false"/>
+ <item name="Inner Clade Labels" type="CheckBox" property="showCladeLabels" value="false"/>
+ </item>
+ <item name="Style">
+ <item name="Text Angle" type="NumberScroller" property="textRotation" increment=".5" default="0" min="-45" max="45"/>
+ <item name="Node Size" type="NumberScroller" property="nodeSize" increment =".005" default=".2" min="0" max=".5"/>
+ <item name="Line Weight" type="NumberScroller" property="lineSize" increment =".001" default=".1" min="0" max=".5"/>
+ </item>
+ <item name="Render Threshold" type="NumberScroller" property="renderThreshold" increment="5" default="150" min="5" max="1000"/>
+ <item name="Minimum Text Size" type="NumberScroller" property="minTextSize" increment =".1" default="10" min="0" max="36"/>
+ <!-- <item name="Stretch Tree to Fit" type="CheckBox" property="fitTreeToWindow" /> -->
+ <item name="Use Branch Lengths" type="CheckBox" property="useBranchLengths" shortcut="ctrl-b" />
+ </item>
+ <!--item name="Tree">
+ <item name="Mutate Once" action="treeMutateOnce" shortcut="control-m"/>
+ <item name="Mutate Slow" action="treeMutateSlow"/>
+ <item name="Mutate Fast" action="treeMutateFast"/>
+ <item name="Stop Mutating" action="treeStopMutating" shortcut="control-shift-m"/>
+ </item>
+ <item name="Flip Tree" action="treeFlip" shortcut="control-R"/>
+ <item name="Auto-sort Tree" action="treeAutoSort" shortcut="control-L"/>
+ <item name="Remove Elbows" action="treeRemoveElbows" shortcut="control-E"/>
+ </item-->
+ </menu>
+
+ <menu name="dock" type="ToolDock" width="30" rotation="left">
+ <!-- the "rotation" parameter can have the values: left, right, top, bottom -->
+ <item name="Arrow" tool="arrow" shortcut="a" icon="dock/arrow.png"/>
+ <item name="Scroll" tool="scroll" shortcut="s" icon="dock/grab.png"/>
+ <item name="Zoom" tool="zoom" shortcut="z" icon="dock/zoom.png"/>
+ </menu>
+
+ <menu name="context" type="org.phylowidget.ui.PhyloContextMenu">
+ <!--item name="Tree Edit" hint="t">
+ <item name="Add" hint="a">
+ <item name="Child" action="nodeAddChild" hint="c"/>
+ <item name="Sister" action="nodeAddSister" hint="s"/>
+ </item>
+ <item name="Delete" hint="d">
+ <item name="This node" action="nodeDelete" hint="t"/>
+ <item name="Subtree" action="nodeDeleteSubtree" hint="s"/>
+ </item>
+ </item-->
+ <item name="Layout" hint="a">
+ <item name="Reroot" action="nodeReroot" hint="r"/>
+ <item name="Flip subtree" action="nodeFlipSubtree" hint="f"/>
+ <item name="Switch children" action="nodeSwitchChildren" hint="s"/>
+ </item>
+ <!--item name="Clipboard" hint="c">
+ <item name="Cut" action="nodeCut" hint="x"/>
+ <item name="Copy" action="nodeCopy" hint="c"/>
+ <item name="Paste" action="nodePaste" hint="v"/>
+ <item name="Clear" action="nodeClearClipboard" hint="r"/>
+ </item-->
+ <!--item name="Node Edit" hint="e">
+ <item name="Name" action="nodeEditName" hint="n"/>
+ <item name="Branch length" action="nodeEditBranchLength" hint="b"/>
+ </item-->
+ </menu>
+</menuset>
Deleted: trunk/treebase-phylowidget/data/menus/nondb-menus.xml
===================================================================
--- trunk/treebase-phylowidget/data/menus/nondb-menus.xml 2010-03-27 01:02:51 UTC (rev 658)
+++ trunk/treebase-phylowidget/data/menus/nondb-menus.xml 2010-03-29 19:34:59 UTC (rev 659)
@@ -1,81 +0,0 @@
-<menuset name="PhyloWidget Menus">
- <menu type="Toolbar" fontsize="11" x="2" y="2">
- <item name="File">
- <!--item name="New Tree" action="treeNew" shortcut="control-n"/-->
- <!--item name="Load Tree..." action="treeLoad"/-->
- <item name="Save Tree..." action="treeSave"/>
- <!--item name="Save Tree To Database" action="treeSaveToDB"/-->
- <item name="Export Image">
- <item name="Large (1600x1200)" action="fileOutputBig"/>
- <item name="Small (640 x 480)" action="fileOutputSmall"/>
- <item name="PDF" action="fileOutputPDF"/>
- </item>
- </item>
- <item name="View">
- <item name="Zoom to Full" action="viewZoomToFull" shortcut="control-F"/>
- <item name="Renderer Type">
- <item name="Rectangular" action="viewRectangular" shortcut="control-1"/>
- <item name="Diagonal" action="viewDiagonal" shortcut="control-2"/>
- <item name="Circular" action="viewCircular" shortcut="control-3"/>
- </item>
- <item name="Show/Hide">
- <item name="Branch Lengths" type="CheckBox" property="showBranchLengths" value="false"/>
- <item name="Inner Clade Labels" type="CheckBox" property="showCladeLabels" value="false"/>
- </item>
- <item name="Style">
- <item name="Text Angle" type="NumberScroller" property="textRotation" increment=".5" default="0" min="-45" max="45"/>
- <item name="Node Size" type="NumberScroller" property="nodeSize" increment =".005" default=".2" min="0" max=".5"/>
- <item name="Line Weight" type="NumberScroller" property="lineSize" increment =".001" default=".1" min="0" max=".5"/>
- </item>
- <item name="Render Threshold" type="NumberScroller" property="renderThreshold" increment="5" default="150" min="5" max="1000"/>
- <item name="Minimum Text Size" type="NumberScroller" property="minTextSize" increment =".1" default="10" min="0" max="36"/>
- <!-- <item name="Stretch Tree to Fit" type="CheckBox" property="fitTreeToWindow" /> -->
- <item name="Use Branch Lengths" type="CheckBox" property="useBranchLengths" shortcut="ctrl-b" />
- </item>
- <!--item name="Tree">
- <item name="Mutate Once" action="treeMutateOnce" shortcut="control-m"/>
- <item name="Mutate Slow" action="treeMutateSlow"/>
- <item name="Mutate Fast" action="treeMutateFast"/>
- <item name="Stop Mutating" action="treeStopMutating" shortcut="control-shift-m"/>
- </item>
- <item name="Flip Tree" action="treeFlip" shortcut="control-R"/>
- <item name="Auto-sort Tree" action="treeAutoSort" shortcut="control-L"/>
- <item name="Remove Elbows" action="treeRemoveElbows" shortcut="control-E"/>
- </item-->
- </menu>
-
- <menu name="dock" type="ToolDock" width="30" rotation="left">
- <!-- the "rotation" parameter can have the values: left, right, top, bottom -->
- <item name="Arrow" tool="arrow" shortcut="a" icon="dock/arrow.png"/>
- <item name="Scroll" tool="scroll" shortcut="s" icon="dock/grab.png"/>
- <item name="Zoom" tool="zoom" shortcut="z" icon="dock/zoom.png"/>
- </menu>
-
- <menu name="context" type="org.phylowidget.ui.PhyloContextMenu">
- <!--item name="Tree Edit" hint="t">
- <item name="Add" hint="a">
- <item name="Child" action="nodeAddChild" hint="c"/>
- <item name="Sister" action="nodeAddSister" hint="s"/>
- </item>
- <item name="Delete" hint="d">
- <item name="This node" action="nodeDelete" hint="t"/>
- <item name="Subtree" action="nodeDeleteSubtree" hint="s"/>
- </item>
- </item-->
- <item name="Layout" hint="a">
- <item name="Reroot" action="nodeReroot" hint="r"/>
- <item name="Flip subtree" action="nodeFlipSubtree" hint="f"/>
- <item name="Switch children" action="nodeSwitchChildren" hint="s"/>
- </item>
- <!--item name="Clipboard" hint="c">
- <item name="Cut" action="nodeCut" hint="x"/>
- <item name="Copy" action="nodeCopy" hint="c"/>
- <item name="Paste" action="nodePaste" hint="v"/>
- <item name="Clear" action="nodeClearClipboard" hint="r"/>
- </item-->
- <!--item name="Node Edit" hint="e">
- <item name="Name" action="nodeEditName" hint="n"/>
- <item name="Branch length" action="nodeEditBranchLength" hint="b"/>
- </item-->
- </menu>
-</menuset>
Modified: trunk/treebase-web/src/main/resources/ApplicationResources.properties
===================================================================
--- trunk/treebase-web/src/main/resources/ApplicationResources.properties 2010-03-27 01:02:51 UTC (rev 658)
+++ trunk/treebase-web/src/main/resources/ApplicationResources.properties 2010-03-29 19:34:59 UTC (rev 659)
@@ -91,6 +91,7 @@
nav.references=References
nav.journals=Journals
+
#-- top navigation menu --
nav.personalinfo = Personal Information
nav.submissions=TreeBASE Submissions
Modified: trunk/treebase-web/src/main/webapp/test/phylowidget/PhyloWidget.jar
===================================================================
(Binary files differ)
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