From: Jim Procter Date: Thu, 2 Jun 2022 16:23:47 +0000 (+0100) Subject: minimal fixes - probably not valid since forester jar out of sync X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=2604ed9c9ad23a7c97b5d885249d81948cbac130 minimal fixes - probably not valid since forester jar out of sync --- diff --git a/j11lib/forester.jar b/j11lib/forester.jar new file mode 100644 index 0000000..afe77b2 Binary files /dev/null and b/j11lib/forester.jar differ diff --git a/j8lib/forester.jar b/j8lib/forester.jar new file mode 100644 index 0000000..afe77b2 Binary files /dev/null and b/j8lib/forester.jar differ diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index a71d75f..89f4036 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -20,86 +20,6 @@ */ package jalview.gui; -import java.util.Locale; -import jalview.analysis.AlignmentSorter; -import jalview.analysis.AlignmentUtils; -import jalview.analysis.CrossRef; -import jalview.analysis.Dna; -import jalview.analysis.ParseProperties; -import jalview.analysis.SequenceIdMatcher; -import jalview.analysis.TreeModel; -import jalview.api.AlignExportSettingI; -import jalview.api.AlignViewControllerGuiI; -import jalview.api.AlignViewControllerI; -import jalview.api.AlignViewportI; -import jalview.api.AlignmentViewPanel; -import jalview.api.FeatureSettingsControllerI; -import jalview.api.SplitContainerI; -import jalview.api.ViewStyleI; -import jalview.bin.Cache; -import jalview.bin.Jalview; -import jalview.commands.CommandI; -import jalview.commands.EditCommand; -import jalview.commands.EditCommand.Action; -import jalview.commands.OrderCommand; -import jalview.commands.RemoveGapColCommand; -import jalview.commands.RemoveGapsCommand; -import jalview.commands.SlideSequencesCommand; -import jalview.commands.TrimRegionCommand; -import jalview.datamodel.AlignedCodonFrame; -import jalview.datamodel.Alignment; -import jalview.datamodel.AlignmentAnnotation; -import jalview.datamodel.AlignmentExportData; -import jalview.datamodel.AlignmentI; -import jalview.datamodel.AlignmentOrder; -import jalview.datamodel.AlignmentView; -import jalview.datamodel.ColumnSelection; -import jalview.datamodel.HiddenColumns; -import jalview.datamodel.HiddenSequences; -import jalview.datamodel.PDBEntry; -import jalview.datamodel.SeqCigar; -import jalview.datamodel.Sequence; -import jalview.datamodel.SequenceGroup; -import jalview.datamodel.SequenceI; -import jalview.ext.archaeopteryx.AptxInit; -import jalview.ext.forester.io.SupportedTreeFileFilter; -import jalview.ext.forester.io.TreeParser; -import jalview.gui.ColourMenuHelper.ColourChangeListener; -import jalview.gui.ViewSelectionMenu.ViewSetProvider; -import jalview.io.AlignmentProperties; -import jalview.io.AnnotationFile; -import jalview.io.BioJsHTMLOutput; -import jalview.io.DataSourceType; -import jalview.io.FileFormat; -import jalview.io.FileFormatI; -import jalview.io.FileFormats; -import jalview.io.FileLoader; -import jalview.io.FileParse; -import jalview.io.FormatAdapter; -import jalview.io.HtmlSvgOutput; -import jalview.io.IdentifyFile; -import jalview.io.JPredFile; -import jalview.io.JalviewFileChooser; -import jalview.io.JalviewFileView; -import jalview.io.JnetAnnotationMaker; -import jalview.io.NewickFile; -import jalview.io.ScoreMatrixFile; -import jalview.io.TCoffeeScoreFile; -import jalview.jbgui.GAlignFrame; -import jalview.schemes.ColourSchemeI; -import jalview.schemes.ColourSchemes; -import jalview.schemes.ResidueColourScheme; -import jalview.schemes.TCoffeeColourScheme; -import jalview.util.MessageManager; -import jalview.viewmodel.AlignmentViewport; -import jalview.viewmodel.ViewportRanges; -import jalview.ws.DBRefFetcher; -import jalview.ws.DBRefFetcher.FetchFinishedListenerI; -import jalview.ws.jws1.Discoverer; -import jalview.ws.jws2.Jws2Discoverer; -import jalview.ws.jws2.jabaws2.Jws2Instance; -import jalview.ws.seqfetcher.DbSourceProxy; - import java.awt.BorderLayout; import java.awt.Color; import java.awt.Component; @@ -139,13 +59,14 @@ import java.util.Deque; import java.util.Enumeration; import java.util.Hashtable; import java.util.List; +import java.util.Locale; import java.util.StringTokenizer; import java.util.Vector; import javax.swing.ButtonGroup; import javax.swing.JCheckBoxMenuItem; -import javax.swing.JComponent; import javax.swing.JComboBox; +import javax.swing.JComponent; import javax.swing.JEditorPane; import javax.swing.JInternalFrame; import javax.swing.JLabel; @@ -164,6 +85,7 @@ import jalview.analysis.Dna; import jalview.analysis.GeneticCodeI; import jalview.analysis.ParseProperties; import jalview.analysis.SequenceIdMatcher; +import jalview.analysis.TreeModel; import jalview.api.AlignExportSettingsI; import jalview.api.AlignViewControllerGuiI; import jalview.api.AlignViewControllerI; @@ -173,7 +95,6 @@ import jalview.api.FeatureSettingsControllerI; import jalview.api.FeatureSettingsModelI; import jalview.api.SplitContainerI; import jalview.api.ViewStyleI; -import jalview.api.analysis.SimilarityParamsI; import jalview.bin.Cache; import jalview.bin.Console; import jalview.bin.Jalview; @@ -200,6 +121,9 @@ import jalview.datamodel.SeqCigar; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; +import jalview.ext.archaeopteryx.AptxInit; +import jalview.ext.forester.io.SupportedTreeFileFilter; +import jalview.ext.forester.io.TreeParser; import jalview.gui.ColourMenuHelper.ColourChangeListener; import jalview.gui.ViewSelectionMenu.ViewSetProvider; import jalview.io.AlignmentProperties; @@ -4230,18 +4154,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, JvOptionPane.WARNING_MESSAGE); ex.printStackTrace(); } - if (fin != null && fin.hasWarningMessage()) - { - JvOptionPane.showMessageDialog(Desktop.desktop, - fin.getWarningMessage(), - MessageManager.getString( - "label.possible_problem_with_tree_file"), - JvOptionPane.WARNING_MESSAGE); - } +// TODO: handle any other warnings from treeParser ? + // if (treeParser != null && treeParser.fin.hasWarningMessage()) +// { +// JvOptionPane.showMessageDialog(Desktop.desktop, +// fin.getWarningMessage(), +// MessageManager.getString( +// "label.possible_problem_with_tree_file"), +// JvOptionPane.WARNING_MESSAGE); +// } } }); chooser.showOpenDialog(this); - } } /** diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java index 042147f..a163c15 100755 --- a/src/jalview/gui/TreePanel.java +++ b/src/jalview/gui/TreePanel.java @@ -24,6 +24,7 @@ import java.util.Locale; import jalview.analysis.AlignmentSorter; import jalview.analysis.TreeModel; +import jalview.api.analysis.SimilarityParamsI; import jalview.bin.Cache; import jalview.bin.Console; import jalview.commands.CommandI; @@ -776,12 +777,6 @@ public void buildTreeCanvas(AlignmentPanel ap) { } else { - /* - * i18n description of Neighbour Joining or Average Distance method - */ - String treecalcnm = MessageManager - .getString("label.tree_calc_" + treeType.toLowerCase()); - /* * i18n description of Neighbour Joining or Average Distance method */ @@ -791,7 +786,7 @@ public void buildTreeCanvas(AlignmentPanel ap) { /* * short score model name (long description can be too long) */ - String smn = scoreModelName; + String smn = substitutionMatrix; /* * put them together as Using diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java index a283691..d3f833f 100755 --- a/src/jalview/io/NewickFile.java +++ b/src/jalview/io/NewickFile.java @@ -488,7 +488,7 @@ public class NewickFile extends FileParse try { distance = (Float.valueOf(ndist.stringMatched(1))).floatValue(); - HasDistances = true; + hasDistances = true; nodehasdistance = true; } catch (Exception e) {