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 (file)
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 (file)
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 (file)
--- 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 (executable)
--- 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 <method> Using <model>

diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java
index a283691..d3f833f 100755 (executable)
--- 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)
           {