diff --git a/src/dr/app/tools/treeannotator/TreeAnnotator.java b/src/dr/app/tools/treeannotator/TreeAnnotator.java index 5c2cf738d2..9d08573f08 100644 --- a/src/dr/app/tools/treeannotator/TreeAnnotator.java +++ b/src/dr/app/tools/treeannotator/TreeAnnotator.java @@ -521,23 +521,21 @@ private void annotateTargetTree(CladeSystem cladeSystem, HeightsSummary heightsO } private void setNodeHeightsCA(CladeSystem cladeSystem, MutableTree targetTree) { - assert false : "Implement this"; - - long startTime = System.currentTimeMillis(); - - progressStream.println("Setting node heights..."); - progressStream.println("0 25 50 75 100"); - progressStream.println("|--------------|--------------|--------------|--------------|"); - - int stepSize = totalTrees / 60; - if (stepSize < 1) stepSize = 1; - + throw new UnsupportedOperationException("CA node heights is not supported in treeannotator X"); +// long startTime = System.currentTimeMillis(); +// progressStream.println("Setting node heights..."); +// progressStream.println("0 25 50 75 100"); +// progressStream.println("|--------------|--------------|--------------|--------------|"); +// +// int stepSize = totalTrees / 60; +// if (stepSize < 1) stepSize = 1; +// // CAHeights caHeights = new CAHeights(this); // caHeights.setTreeHeightsByCA(targetTree, inputFileName, burnin); - - long timeElapsed = (System.currentTimeMillis() - startTime) / 1000; - progressStream.println("* [" + timeElapsed + " secs]"); - progressStream.println(); +// +// long timeElapsed = (System.currentTimeMillis() - startTime) / 1000; +// progressStream.println("* [" + timeElapsed + " secs]"); +// progressStream.println(); } private void writeAnnotatedTree(String outputFileName, MutableTree targetTree) { @@ -589,9 +587,10 @@ public static void printUsage(Arguments arguments) { arguments.printUsage("treeannotator", " []"); progressStream.println(); - progressStream.println(" Example: treeannotator test.trees out.txt"); - progressStream.println(" Example: treeannotator -burnin 100 -heights mean test.trees out.txt"); - progressStream.println(" Example: treeannotator -burnin 100 -target map.tree test.trees out.txt"); + progressStream.println(" Example: treeannotator test.trees out.tree"); + progressStream.println(" Example: treeannotator --burnin 100 --heights mean test.trees out.tree"); + progressStream.println(" Example: treeannotator --type hipstr --burnin 100 --heights mean test.trees out.tree"); + progressStream.println(" Example: treeannotator -b 100 -tf map.tree test.trees out.tree"); progressStream.println(); } @@ -644,7 +643,7 @@ public static void main(String[] args) throws IOException { } final String versionString = VERSION.getVersionString(); - String nameString = "TreeAnnotator " + versionString; + String nameString = "TreeAnnotatorX " + versionString; String aboutString = "

" + versionString + ", " + VERSION.getDateString() + "

" + "

by
" + "Andrew Rambaut and Alexei J. Drummond

" + @@ -666,7 +665,7 @@ public static void main(String[] args) throws IOException { TreeAnnotatorDialog dialog = new TreeAnnotatorDialog(new JFrame()); - if (!dialog.showDialog("TreeAnnotator " + versionString)) { + if (!dialog.showDialog("TreeAnnotatorX " + versionString)) { return; } @@ -766,10 +765,9 @@ public static void main(String[] args) throws IOException { } else if (value.equalsIgnoreCase("median")) { heights = HeightsSummary.MEDIAN_HEIGHTS; } else if (value.equalsIgnoreCase("ca")) { - progressStream.println("CA heights are not supported - to avoid negative branch lengths, construct a HIPSTR tree"); + progressStream.println("CA heights are not supported - this has been superseded by the HIPSTR tree (--type hipstr)"); printUsage(arguments); System.exit(1); -// heights = HeightsSummary.CA_HEIGHTS; } }