Details
Description
If jalview 2.11.4.1 runs out of memory whilst building the similarity matrix during the tree calculation, it leaves the window showing and doesn't let the user know.
WARN - Request to http://127.0.0.1:9124 returned java.net.ConnectException: Connection refused (Connection refused)
Exception in thread "Thread-36" java.lang.OutOfMemoryError: Java heap space
at jalview.math.Matrix.<init>(Matrix.java:104)
at jalview.analysis.scoremodels.ScoreMatrix.findSimilarities(ScoreMatrix.java:498)
at jalview.analysis.scoremodels.ScoreMatrix.findSimilarities(ScoreMatrix.java:471)
at jalview.analysis.scoremodels.SimilarityScoreModel.findDistances(SimilarityScoreModel.java:40)
at jalview.analysis.TreeBuilder.computeTree(TreeBuilder.java:124)
at jalview.analysis.TreeBuilder.<init>(TreeBuilder.java:78)
at jalview.analysis.AverageDistanceTree.<init>(AverageDistanceTree.java:44)
at jalview.gui.TreePanel$TreeLoader.run(TreePanel.java:392)
Simply needs wrapping with an OOMError try/catch and appropriate warning dialog shown as in other places.
WARN - Request to http://127.0.0.1:9124 returned java.net.ConnectException: Connection refused (Connection refused)
Exception in thread "Thread-36" java.lang.OutOfMemoryError: Java heap space
at jalview.math.Matrix.<init>(Matrix.java:104)
at jalview.analysis.scoremodels.ScoreMatrix.findSimilarities(ScoreMatrix.java:498)
at jalview.analysis.scoremodels.ScoreMatrix.findSimilarities(ScoreMatrix.java:471)
at jalview.analysis.scoremodels.SimilarityScoreModel.findDistances(SimilarityScoreModel.java:40)
at jalview.analysis.TreeBuilder.computeTree(TreeBuilder.java:124)
at jalview.analysis.TreeBuilder.<init>(TreeBuilder.java:78)
at jalview.analysis.AverageDistanceTree.<init>(AverageDistanceTree.java:44)
at jalview.gui.TreePanel$TreeLoader.run(TreePanel.java:392)
Simply needs wrapping with an OOMError try/catch and appropriate warning dialog shown as in other places.