JAL-2805 bunch of needed methods/constants made public

diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java
index 3696136..43bc6ad 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Configuration.java
+++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java
@@ -1735,7 +1735,7 @@ public final class Configuration {
         return _species_colors;
     }
 
-    final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
+    public final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
         return _taxonomy_extraction;
     }
 
@@ -1764,11 +1764,11 @@ public final class Configuration {
         return _hide_controls_and_menus;
     }
 
-    boolean isInternalNumberAreConfidenceForNhParsing() {
+    public boolean isInternalNumberAreConfidenceForNhParsing() {
         return _internal_number_are_confidence_for_nh_parsing;
     }
 
-    boolean isReplaceUnderscoresInNhParsing() {
+    public boolean isReplaceUnderscoresInNhParsing() {
         return _nh_parsing_replace_underscores;
     }
 
@@ -1795,7 +1795,7 @@ public final class Configuration {
         return _use_tabbed_display;
     }
 
-    boolean isValidatePhyloXmlAgainstSchema() {
+   public boolean isValidatePhyloXmlAgainstSchema() {
         return _validate_against_phyloxml_xsd_schema;
     }
 

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
index a3a86c4..95a42b8 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
@@ -84,16 +84,16 @@ import org.forester.util.WindowsUtils;
 
 public abstract class MainFrame extends JInternalFrame implements ActionListener {
 
-    final static NHFilter            nhfilter                                = new NHFilter();
-    final static NHXFilter           nhxfilter                               = new NHXFilter();
-    final static XMLFilter           xmlfilter                               = new XMLFilter();
-    final static TolFilter           tolfilter                               = new TolFilter();
-    final static NexusFilter         nexusfilter                             = new NexusFilter();
-    final static PdfFilter           pdffilter                               = new PdfFilter();
-    final static GraphicsFileFilter  graphicsfilefilter                      = new GraphicsFileFilter();
-    final static MsaFileFilter       msafilter                               = new MsaFileFilter();
-    final static SequencesFileFilter seqsfilter                              = new SequencesFileFilter();
-    final static DefaultFilter       defaultfilter                           = new DefaultFilter();
+    public final static NHFilter            nhfilter                                = new NHFilter();
+    public final static NHXFilter           nhxfilter                               = new NHXFilter();
+    public final static XMLFilter           xmlfilter                               = new XMLFilter();
+    public final static TolFilter           tolfilter                               = new TolFilter();
+    public final static NexusFilter         nexusfilter                             = new NexusFilter();
+    public final static PdfFilter           pdffilter                               = new PdfFilter();
+    public final static GraphicsFileFilter  graphicsfilefilter                      = new GraphicsFileFilter();
+    public final static MsaFileFilter       msafilter                               = new MsaFileFilter();
+    public final static SequencesFileFilter seqsfilter                              = new SequencesFileFilter();
+    public final static DefaultFilter       defaultfilter                           = new DefaultFilter();
     static final String              USE_MOUSEWHEEL_SHIFT_TO_ROTATE          = "rotate with mousewheel + Shift (or A and S), D toggles between horizontal and radial labels";
     static final String              PHYLOXML_REF_TOOL_TIP                   = AptxConstants.PHYLOXML_REFERENCE;                                                                                                                                                //TODO //FIXME
     static final String              APTX_REF_TOOL_TIP                       = AptxConstants.APTX_REFERENCE;