Porting changes from branch 1.7 r5109

Author: rambaut

release/common/README.txt

@@ -1,4 +1,4 @@
-                    BEAST v1.7.0 2002-2012
+                    BEAST v1.7.3 2002-2012
         Bayesian Evolutionary Analysis Sampling Trees
                               by
       Alexei J. Drummond, Andrew Rambaut & Marc Suchard
@@ -16,7 +16,7 @@
                       msuchard@ucla.edu
 
 
-Last updated: a.rambaut@ed.ac.uk - 8th February 2012
+Last updated: a.rambaut@ed.ac.uk - 1st Aug 2012
 
 Contents:
 1) INTRODUCTION

release/common/VERSION HISTORY.txt

@@ -1,4 +1,4 @@
-                    BEAST v1.7.1 2002-2012
+                    BEAST v1.7.3 2002-2012
         Bayesian Evolutionary Analysis Sampling Trees
                               by
       Alexei J. Drummond, Andrew Rambaut & Marc Suchard
@@ -17,20 +17,73 @@
 
 
 Version History
-Last updated: a.rambaut@ed.ac.uk - 8th March 2012
+Last updated: a.rambaut@ed.ac.uk - 2nd Aug 2012
 All issues can be viewed at http://code.google.com/p/beast-mcmc/issues/list
 
 ================================================================================
 
-Version 1.7.1 released 9th March 2012
+Version 1.7.3 released XXX XXX 2012
+
+    New Features:
+       Added 'precision' attribute in Date element to allow easy sampling of tip date when the date of sampling is
+            known to a limited precision (see testTipDatePrecision.xml in examples/testXML folder).
+
+	Bug Fixes:
+       Issue 631:	Code generated by BEAUti for substitutions trees doesn't load into BEAST
+       Issue 635:	*BEAST 'species' attributes are being created outside the <taxon> elements
+       Issue 633:	Multivariate continuous trait analyses doesn't respect ancestral state reconstruction choices
+       Issue 636:	Unlinked codons and state reconstruction in BEAUTi
+       Issue 640:	GUI error when canceling species-tree analysis
+       Issue 642:	Inappropriate default values provided for microsatellite model parameters in BEAUti
+       Issue 643:	Unable to specify a MRCA node to reconstruct ancestral states
+       Issue 645:	Discrete traits were generating ancestral reconstructions irrespective of the Ancestral States settings
+       Issue 647:	Selecting robust counting was not creating the correct XML
+       Issue 651:	Default Poisson prior for asymmetric BSSVS model of discrete traits is not standard
+       Issue 652:	Some conditioning priors need to be evaluated before the data likelihood
+
+    Other changes:
+       Restored non-BEAGLE AncestralTreeLikelihood availability - should be considered deprecated.
+       Some changes to the default BEAGLE options to help discrete trait models run (SSE is switched off for
+           non-nucleotide partitions and the default scaling scheme is now 'delayed').
+
+================================================================================
+
+Version 1.7.2 released 22th May 2012
+
+	Bug Fixes:
+	   Issue 609:	BEAUti duplicate prefix issue for multi-partition
+	   Issue 611:	BEAUti misnames the rates log file for BSSVS
+	   Issue 612:	BEAUTi robust counting XML was not overriding the default
+	                stripping of ambiguous sites.
+	   Issue 614:	Writing Newick user tree in BEAUti doesn't quote taxa with
+	                space in the name
+       Issue 615:	Multivariate traits generation by BEAUti was broken in
+                    the 1.7.1 update
+       Issue 618:	BEAUti errors in States panel
+       Issue 619:	BEAUti bug: cannot select a defined taxon set in
+                    "Apply to taxon set" at the Tip date sampling
+       Issue 620:	BEAUti only allows taxon sets >1 taxa
+       Issue 621:	r3896 and r4062 broke Skyride in BEAUti
+       Issue 622:	BEAUti: the "big" updown operator is missing for
+                    *BEAST when calibration
+       Issue 623:	Logging multiple branch rate models in same tree log is broken
+       Issue 624:	Check boxes in BEAUti States panel do not line up
+       Issue 625:	BEAUti XML invalid for 1 codon-partitioned partition and any
+                    2nd partition
+       Issue 627:	Error renaming clock-group
+       Issue 629:	BEAST doesn't appear to be using multithreading
+
+
+================================================================================
+
+Version 1.7.1 released 16th March 2012
 
     New Features:
        TN93 added to BEAGLE BEAST interface
        Added BEAGLE rescaling options to options dialog
        Added BEAGLE rescaling frequency commandline option
 
 	Bug Fixes:
-	   Issue 71:    Reflected exponentials (or lognormals) as priors?
 	   Issue 571:	TN93 substitution model
        Issue 594:	BEAUti 1.7 has a redundant and non-functional Sequence Error
                     Model popup menu in SiteModelPanel
@@ -49,6 +102,8 @@ Version 1.7.1 released 9th March 2012
                     bound and offset
        Issue 604:	RealNumberField FocusListener in prior dialog makes
                     many popups
+       Issue 605:	BEAUti complains about missing values in traits files
+
 
 
 ================================================================================

src/dr/app/beauti/BeautiFrame.java

@@ -65,8 +65,6 @@
  */
 public class BeautiFrame extends DocumentFrame {
 
-    private static final boolean ENABLE_ANCESTRAL_STATES = true;
-
     private static final long serialVersionUID = 2114148696789612509L;
 
     public final static String DATA_PARTITIONS = "Partitions";
@@ -200,13 +198,13 @@ public void initializeComponents() {
                 "Select the priors on trees including coalescent models<br>" +
                 "birth-death speciation models and the *BEAST gene tree,<br>" +
                 "species tree options.</html>");
-        if (ENABLE_ANCESTRAL_STATES) {
-            tabbedPane.addTab(ANCESTRAL_STATES, ancestralStatesPanel);
-            tabbedPane.setToolTipTextAt(index++, "<html>" +
-                    "Select options for sampling ancestral states at specific<br>" +
-                    "or all common ancestors, models of counting state changes<br>" +
-                    "and models of sequencing error for data partitions.</html>");
-        }
+
+        tabbedPane.addTab(ANCESTRAL_STATES, ancestralStatesPanel);
+        tabbedPane.setToolTipTextAt(index++, "<html>" +
+                "Select options for sampling ancestral states at specific<br>" +
+                "or all common ancestors, models of counting state changes<br>" +
+                "and models of sequencing error for data partitions.</html>");
+
         tabbedPane.addTab(PRIORS, priorsPanel);
         tabbedPane.setToolTipTextAt(index++, "<html>" +
                 "Specify prior probability distributions on each and every<br>" +
@@ -319,9 +317,7 @@ public void setAllOptions() {
             siteModelsPanel.setOptions(options);
             clockModelsPanel.setOptions(options);
             treesPanel.setOptions(options);
-            if (ENABLE_ANCESTRAL_STATES) {
-                ancestralStatesPanel.setOptions(options);
-            }
+            ancestralStatesPanel.setOptions(options);
             priorsPanel.setOptions(options);
             operatorsPanel.setOptions(options);
             mcmcPanel.setOptions(options);
@@ -357,9 +353,7 @@ private void getAllOptions() {
             siteModelsPanel.getOptions(options);
             clockModelsPanel.getOptions(options);
             treesPanel.getOptions(options);
-            if (ENABLE_ANCESTRAL_STATES) {
-                ancestralStatesPanel.getOptions(options);
-            }
+            ancestralStatesPanel.getOptions(options);
             priorsPanel.getOptions(options);
             operatorsPanel.getOptions(options);
             mcmcPanel.getOptions(options);
@@ -677,18 +671,7 @@ public boolean setupStarBEAST(boolean useStarBEAST) {
             tabbedPane.insertTab("Species Sets", null, speciesSetPanel, null, 1);
 
         } else { // remove species
-            // why delete this? The user may want to use it again
-            // because it is how *BEAST reverse to normal BEAST, otherwise after uncheck, everything goes wrong.
-
-            // AR - it is a fundamental point of UI design that we don't delete the user's work.
-            // If the user had hand typed all the species designations in and then just switched *BEAST
-            // off for a moment and lost all that work they would be annoyed. We need to work out what
-            // why turning off *BEAST doesn't fully work.
-
-//            if (options.traitExists(TraitData.TRAIT_SPECIES)) {
-//                traitsPanel.removeTrait(TraitData.TRAIT_SPECIES);
-            options.fileNameStem = MCMCPanel.fileNameStem;
-//            }
+            options.fileNameStem = MCMCPanel.DEFAULT_FILE_NAME_STEM;
 
             tabbedPane.removeTabAt(1);
             tabbedPane.insertTab("Taxon Sets", null, taxonSetPanel, null, 1);

src/dr/app/beauti/mcmcpanel/MCMCPanel.java

@@ -59,13 +59,13 @@ public class MCMCPanel extends BeautiPanel {
 
     JCheckBox samplePriorCheckBox = new JCheckBox("Sample from prior only - create empty alignment");
 
-    public static final String fileNameStem = "untitled";
-    JTextField fileNameStemField = new JTextField(fileNameStem);
+    public static final String DEFAULT_FILE_NAME_STEM = "untitled";
+    JTextField fileNameStemField = new JTextField(DEFAULT_FILE_NAME_STEM);
 
     private JCheckBox addTxt = new JCheckBox("Add .txt suffix");
 
-    JTextField logFileNameField = new JTextField(fileNameStem + ".log");
-    JTextField treeFileNameField = new JTextField(fileNameStem + "." + STARBEASTOptions.TREE_FILE_NAME);
+    JTextField logFileNameField = new JTextField(DEFAULT_FILE_NAME_STEM + ".log");
+    JTextField treeFileNameField = new JTextField(DEFAULT_FILE_NAME_STEM + "." + STARBEASTOptions.TREE_FILE_NAME);
 //    JCheckBox allowOverwriteLogCheck = new JCheckBox("Allow to overwrite the existing log file");
 
 //    JCheckBox mapTreeLogCheck = new JCheckBox("Create tree file containing the MAP tree:");
@@ -75,7 +75,7 @@ public class MCMCPanel extends BeautiPanel {
     JTextField substTreeFileNameField = new JTextField("untitled(subst).trees");
 
     JCheckBox operatorAnalaysisCheck = new JCheckBox("Create operator analysis file:");
-    JTextField operatorAnalaysisFileNameField = new JTextField(fileNameStem + ".ops");
+    JTextField operatorAnalaysisFileNameField = new JTextField(DEFAULT_FILE_NAME_STEM + ".ops");
 
     BeautiFrame frame = null;
     private final OptionsPanel optionsPanel;
@@ -323,7 +323,7 @@ public void setOptions(BeautiOptions options) {
         if (options.fileNameStem != null) {
             fileNameStemField.setText(options.fileNameStem);
         } else {
-            fileNameStemField.setText(fileNameStem);
+            fileNameStemField.setText(DEFAULT_FILE_NAME_STEM);
             fileNameStemField.setEnabled(false);
         }
 
@@ -387,8 +387,8 @@ private void updateOtherFileNames(BeautiOptions options) {
         } else {
 //            fileNameStemField.setText(fileNameStem);
 //            fileNameStemField.setEnabled(false);
-            logFileNameField.setText(fileNameStem + ".log");
-            treeFileNameField.setText(fileNameStem + "." + STARBEASTOptions.TREE_FILE_NAME);
+            logFileNameField.setText(DEFAULT_FILE_NAME_STEM + ".log");
+            treeFileNameField.setText(DEFAULT_FILE_NAME_STEM + "." + STARBEASTOptions.TREE_FILE_NAME);
 //            mapTreeLogCheck.setEnabled(false);
 //            mapTreeFileNameField.setEnabled(false);
 //            mapTreeFileNameField.setText("untitled");

src/dr/app/beauti/options/BeautiOptions.java

@@ -114,7 +114,7 @@ public void reset() {
         generateCSV = true;  // until/if a button
         samplePriorOnly = false;
 
-        fileNameStem = MCMCPanel.fileNameStem;
+        fileNameStem = MCMCPanel.DEFAULT_FILE_NAME_STEM;
         logFileName = null;
         allowOverwriteLog = false;
 //        mapTreeLog = false;
@@ -1226,7 +1226,7 @@ public int getSpeciesIndex(String speciesName) {
     public boolean generateCSV = true;  // until/if a button
     public boolean samplePriorOnly = false;
 
-    public String fileNameStem = MCMCPanel.fileNameStem;
+    public String fileNameStem = MCMCPanel.DEFAULT_FILE_NAME_STEM;
     public String logFileName = null;
     public boolean allowOverwriteLog = false;
     //    public boolean mapTreeLog = false;

src/dr/app/beauti/util/BEAUTiImporter.java

@@ -26,6 +26,7 @@
 package dr.app.beauti.util;
 
 import dr.app.beauti.BeautiFrame;
+import dr.app.beauti.mcmcpanel.MCMCPanel;
 import dr.app.beauti.options.*;
 import dr.app.util.Utils;
 import dr.evolution.alignment.Alignment;
@@ -519,7 +520,7 @@ private void setData(String fileName, Taxa taxonList, Patterns patterns,
     ) throws ImportException, IllegalArgumentException {
         String fileNameStem = Utils.trimExtensions(fileName,
                 new String[]{"NEX", "NEXUS", "TRE", "TREE", "XML", "TXT"});
-        if (options.fileNameStem == null) {
+        if (options.fileNameStem == null || options.fileNameStem.equals(MCMCPanel.DEFAULT_FILE_NAME_STEM)) {
             options.fileNameStem = fileNameStem;
         }