Merge branch 'develop' into documentation/JAL-2418_release2102

diff --git a/examples/exampleFeatures.txt b/examples/exampleFeatures.txt
index 5b65810..cc159d1 100755 (executable)
--- a/examples/exampleFeatures.txt
+++ b/examples/exampleFeatures.txt
@@ -1,5 +1,5 @@
 ST-TURN-IIL    blue
-GAMMA-TURN-CLASSIC     gray
+GAMMA-TURN-CLASSIC     lightGray
 BETA-TURN-IR   9a6a94
 BETA-TURN-IL   d6a6ca
 BETA-BULGE     1dc451

diff --git a/help/html/releases.html b/help/html/releases.html
index eff80b5..5376db8 100755 (executable)
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -77,7 +77,9 @@ li:before {
       <td><div align="left">
           <em>General</em>
           <ul>
-          <li><!-- JAL-2360,JAL-2371, -->More robust colours and shader model for alignments and groups</li>
+                 <li><!-- JAL-2379 -->Revised implementation of PCA for speed and memory efficiency (~30x faster)</li>
+                 <li><!-- JAL-2500 -->Trees computed on Sequence Feature Similarity may have different topology due to increased precision</li>
+                 <li><!-- JAL-2360,JAL-2371, -->More robust colours and shader model for alignments and groups</li>
           <li><!--  JAL-384 -->Custom shading schemes created via groovy scripts</li>
           <li><!--  JAL-2491 -->linked scrolling of CDS/Protein views via Overview or sequence motif search operations</li>
           <li><!--  JAL-2526 -->Efficiency improvements for interacting with alignment and overview windows</li>
@@ -119,9 +121,14 @@ li:before {
           <li><!--  --></li>
           </ul>
           <em>Test Suite</em>
+          <ul>
           <li><!--  JAL-2474 -->Added PrivilegedAccessor to test suite</li>
           <li><!-- JAL-2326 -->Prevent or clear modal dialogs raised during tests</li>
           <li><!--  -->  
+          <em>Scripting</em>
+          <ul>
+                       <li><!-- JAL-2344 -->FileFormatI interface for describing and identifying file formats (instead of String constants)</li>
+          </ul>
           </ul>
           </div></td><td><div align="left">
           <em>General</em>
@@ -171,6 +178,12 @@ li:before {
            <li><!-- JAL-2034 -->Overview window doesn't always update when a group defined on the alignment is resized</li>
            <li><!-- JAL-2605 -->Mouseovers on left/right scale region in wrapped view result in positional status updates</li>
            <li><!-- JAL-2563 -->Status bar shows position for ambiguous amino acid and nucleotide symbols</li>
+           <li><!-- JAL-2602 -->Copy consensus sequence failed if alignment included gapped columns</li>
+           <li><!-- JAL-2589 -->User defined gap colour not shown in overview when features overlaid on alignment</li>
+           </ul>
+             <strong>Documentation</strong>
+             <ul>
+               <li><!-- JAL-2339 -->Release notes reformatted for readibility with the built-in Java help viewer</li>
           </ul>
           <em>Application</em>
           <ul>
@@ -195,9 +208,11 @@ li:before {
             <li><!-- JAL-2563 -->Status bar doesn't show positions for ambiguous amino acids</li>
           <li><!-- JAL-2291 -->Hide insertions in PopUp menu excludes gaps in selection, current sequence and only within selected columns</li>
          <li><!-- JAL-2582 -->Cannot retrieve protein products from Ensembl by Peptide ID</li>
+         <li><!-- JAL-2431 -->cDNA Consensus annotation not shown in CDS/Protein view after CDS sequences added for aligned proteins</li>
           </ul>
           <em>Applet</em>
           <ul>
+          <li><!-- JAL-2468 -->Switching between Nucleotide and Protein score models doesn't always result in an updated PCA plot</li>
           <li><!-- JAL-2442 -->Features not rendered as transparent on overview or linked structure view</li> 
           <li><!--  JAL-2372 -->Colour group by conservation doesn't work (since 2.8)</li>
           <li><!-- JAL-2517 -->Hitting Cancel after applying user-defined colourscheme doesn't restore original colourscheme</li>
@@ -208,7 +223,10 @@ li:before {
           <li><!-- JAL-2550 -->Importing annotation file with rows containing just upper and lower case letters are interpreted as WUSS rna secondary structure symbols</li>  
             <li><!-- JAL-2590 -->Cannot load Newick trees from eggnog ortholog database</li>
           </ul>
-          
+          <em>Test Suite</em>
+          <ul><li><!-- JAL-2314 -->Unit test failure: jalview.ws.jabaws.RNAStructExportImport setup fails</li>
+          <li><!-- JAL- --></li>
+          </ul>
           </div>
     <tr>
       <td width="60" nowrap>

diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html
index 4b82179..8a0436d 100755 (executable)
--- a/help/html/whatsNew.html
+++ b/help/html/whatsNew.html
@@ -32,6 +32,15 @@
     highlights are below.
   </p>
   <ul>
+    <li><strong>New UI, and faster and more configurable implementation for PCA, Neighbour-Joining and UPGMA Trees</strong><br>
+      Menu entries for calculating PCA and different types of tree have
+      been replaced by a single <em>Calculations</em> dialog box. The
+      underlying implementation for the PCA and tree calculations have been
+      made faster and more memory efficient. A new framework has also been
+      created for the score models used to calculate distances between
+      sequences. This framework allows import of substitution matrices in
+      NCBI and AAIndex format, and custom score models to be created via a
+      groovy script.</li>
     <li><strong>Update to JABAWS 2.2</strong><br />Jalview's
       alignment, protein conservation analysis, and protein disorder and
       RNA secondary structure prediction services are now provided by <a

diff --git a/src/jalview/gui/FontChooser.java b/src/jalview/gui/FontChooser.java
index 20a6289..06f29e9 100755 (executable)
--- a/src/jalview/gui/FontChooser.java
+++ b/src/jalview/gui/FontChooser.java
@@ -323,17 +323,22 @@ public class FontChooser extends GFontChooser
       ap.fontChanged();
 
       /*
-       * adjust other half of split frame if present, whether or not same font or
-       * scale to cDNA is selected, because a font change may affect character
-       * width, and this is kept the same in both panels
+       * adjust other half of split frame if any, if either same
+       * font, or proportionate scaling, is selected
        */
-      if (fontAsCdna.isVisible())
+      if (fontAsCdna.isEnabled())
       {
         if (fontAsCdna.isSelected())
         {
+          /*
+           * copy the font
+           */
           ap.av.getCodingComplement().setFont(newFont, true);
         }
 
+        /*
+         * adjust layout for font change / reset / sizing
+         */
         SplitFrame splitFrame = (SplitFrame) ap.alignFrame
                 .getSplitViewContainer();
         splitFrame.adjustLayout();

diff --git a/utils/eclipse/JalviewCodeStyle.xml b/utils/eclipse/JalviewCodeStyle.xml
index b84b083..7b93801 100644 (file)
--- a/utils/eclipse/JalviewCodeStyle.xml
+++ b/utils/eclipse/JalviewCodeStyle.xml
@@ -22,11 +22,11 @@
 <profiles version="12">
 <profile kind="CodeFormatterProfile" name="Jalview" version="12">
 <setting id="org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode" value="enabled"/>
-<setting id="org.eclipse.jdt.core.compiler.codegen.targetPlatform" value="1.5"/>
-<setting id="org.eclipse.jdt.core.compiler.compliance" value="1.5"/>
+<setting id="org.eclipse.jdt.core.compiler.codegen.targetPlatform" value="1.8"/>
+<setting id="org.eclipse.jdt.core.compiler.compliance" value="1.8"/>
 <setting id="org.eclipse.jdt.core.compiler.problem.assertIdentifier" value="error"/>
 <setting id="org.eclipse.jdt.core.compiler.problem.enumIdentifier" value="error"/>
-<setting id="org.eclipse.jdt.core.compiler.source" value="1.5"/>
+<setting id="org.eclipse.jdt.core.compiler.source" value="1.8"/>
 <setting id="org.eclipse.jdt.core.formatter.align_type_members_on_columns" value="false"/>
 <setting id="org.eclipse.jdt.core.formatter.alignment_for_arguments_in_allocation_expression" value="16"/>
 <setting id="org.eclipse.jdt.core.formatter.alignment_for_arguments_in_annotation" value="52"/>
@@ -38,18 +38,20 @@
 <setting id="org.eclipse.jdt.core.formatter.alignment_for_binary_expression" value="16"/>
 <setting id="org.eclipse.jdt.core.formatter.alignment_for_compact_if" value="16"/>
 <setting id="org.eclipse.jdt.core.formatter.alignment_for_conditional_expression" value="80"/>
-<setting id="org.eclipse.jdt.core.formatter.alignment_for_enum_constants" value="0"/>
+<setting id="org.eclipse.jdt.core.formatter.alignment_for_enum_constants" value="16"/>
 <setting id="org.eclipse.jdt.core.formatter.alignment_for_expressions_in_array_initializer" value="16"/>
 <setting id="org.eclipse.jdt.core.formatter.alignment_for_method_declaration" value="0"/>
 <setting id="org.eclipse.jdt.core.formatter.alignment_for_multiple_fields" value="16"/>
 <setting id="org.eclipse.jdt.core.formatter.alignment_for_parameters_in_constructor_declaration" value="16"/>
 <setting id="org.eclipse.jdt.core.formatter.alignment_for_parameters_in_method_declaration" value="16"/>
+<setting id="org.eclipse.jdt.core.formatter.alignment_for_resources_in_try" value="80"/>
 <setting id="org.eclipse.jdt.core.formatter.alignment_for_selector_in_method_invocation" value="16"/>
 <setting id="org.eclipse.jdt.core.formatter.alignment_for_superclass_in_type_declaration" value="16"/>
 <setting id="org.eclipse.jdt.core.formatter.alignment_for_superinterfaces_in_enum_declaration" value="16"/>
 <setting id="org.eclipse.jdt.core.formatter.alignment_for_superinterfaces_in_type_declaration" value="16"/>
 <setting id="org.eclipse.jdt.core.formatter.alignment_for_throws_clause_in_constructor_declaration" value="16"/>
 <setting id="org.eclipse.jdt.core.formatter.alignment_for_throws_clause_in_method_declaration" value="16"/>
+<setting id="org.eclipse.jdt.core.formatter.alignment_for_union_type_in_multicatch" value="16"/>
 <setting id="org.eclipse.jdt.core.formatter.blank_lines_after_imports" value="1"/>
 <setting id="org.eclipse.jdt.core.formatter.blank_lines_after_package" value="1"/>
 <setting id="org.eclipse.jdt.core.formatter.blank_lines_before_field" value="1"/>
@@ -64,17 +66,18 @@
 <setting id="org.eclipse.jdt.core.formatter.brace_position_for_annotation_type_declaration" value="next_line"/>
 <setting id="org.eclipse.jdt.core.formatter.brace_position_for_anonymous_type_declaration" value="next_line"/>
 <setting id="org.eclipse.jdt.core.formatter.brace_position_for_array_initializer" value="next_line_on_wrap"/>
-<setting id="org.eclipse.jdt.core.formatter.brace_position_for_block_in_case" value="next_line"/>
 <setting id="org.eclipse.jdt.core.formatter.brace_position_for_block" value="next_line"/>
+<setting id="org.eclipse.jdt.core.formatter.brace_position_for_block_in_case" value="next_line"/>
 <setting id="org.eclipse.jdt.core.formatter.brace_position_for_constructor_declaration" value="next_line"/>
 <setting id="org.eclipse.jdt.core.formatter.brace_position_for_enum_constant" value="next_line"/>
 <setting id="org.eclipse.jdt.core.formatter.brace_position_for_enum_declaration" value="next_line"/>
+<setting id="org.eclipse.jdt.core.formatter.brace_position_for_lambda_body" value="end_of_line"/>
 <setting id="org.eclipse.jdt.core.formatter.brace_position_for_method_declaration" value="next_line"/>
 <setting id="org.eclipse.jdt.core.formatter.brace_position_for_switch" value="next_line"/>
 <setting id="org.eclipse.jdt.core.formatter.brace_position_for_type_declaration" value="next_line"/>
 <setting id="org.eclipse.jdt.core.formatter.comment.clear_blank_lines_in_block_comment" value="false"/>
 <setting id="org.eclipse.jdt.core.formatter.comment.clear_blank_lines_in_javadoc_comment" value="false"/>
-<setting id="org.eclipse.jdt.core.formatter.comment.format_block_comments" value="true"/>
+<setting id="org.eclipse.jdt.core.formatter.comment.format_block_comments" value="false"/>
 <setting id="org.eclipse.jdt.core.formatter.comment.format_header" value="false"/>
 <setting id="org.eclipse.jdt.core.formatter.comment.format_html" value="true"/>
 <setting id="org.eclipse.jdt.core.formatter.comment.format_javadoc_comments" value="true"/>
@@ -89,10 +92,10 @@
 <setting id="org.eclipse.jdt.core.formatter.comment.new_lines_at_javadoc_boundaries" value="true"/>
 <setting id="org.eclipse.jdt.core.formatter.comment.preserve_white_space_between_code_and_line_comments" value="false"/>
 <setting id="org.eclipse.jdt.core.formatter.compact_else_if" value="true"/>
-<setting id="org.eclipse.jdt.core.formatter.continuation_indentation_for_array_initializer" value="2"/>
 <setting id="org.eclipse.jdt.core.formatter.continuation_indentation" value="4"/>
-<setting id="org.eclipse.jdt.core.formatter.disabling_tag" value="@formatter\:off"/>
-<setting id="org.eclipse.jdt.core.formatter.enabling_tag" value="@formatter\:on"/>
+<setting id="org.eclipse.jdt.core.formatter.continuation_indentation_for_array_initializer" value="2"/>
+<setting id="org.eclipse.jdt.core.formatter.disabling_tag" value="@formatter:off"/>
+<setting id="org.eclipse.jdt.core.formatter.enabling_tag" value="@formatter:on"/>
 <setting id="org.eclipse.jdt.core.formatter.format_guardian_clause_on_one_line" value="false"/>
 <setting id="org.eclipse.jdt.core.formatter.format_line_comment_starting_on_first_column" value="true"/>
 <setting id="org.eclipse.jdt.core.formatter.indent_body_declarations_compare_to_annotation_declaration_header" value="true"/>
@@ -130,8 +133,8 @@
 <setting id="org.eclipse.jdt.core.formatter.insert_new_line_in_empty_type_declaration" value="insert"/>
 <setting id="org.eclipse.jdt.core.formatter.insert_space_after_and_in_type_parameter" value="insert"/>
 <setting id="org.eclipse.jdt.core.formatter.insert_space_after_assignment_operator" value="insert"/>
-<setting id="org.eclipse.jdt.core.formatter.insert_space_after_at_in_annotation_type_declaration" value="do not insert"/>
 <setting id="org.eclipse.jdt.core.formatter.insert_space_after_at_in_annotation" value="do not insert"/>
+<setting id="org.eclipse.jdt.core.formatter.insert_space_after_at_in_annotation_type_declaration" value="do not insert"/>
 <setting id="org.eclipse.jdt.core.formatter.insert_space_after_binary_operator" value="insert"/>
 <setting id="org.eclipse.jdt.core.formatter.insert_space_after_closing_angle_bracket_in_type_arguments" value="insert"/>
 <setting id="org.eclipse.jdt.core.formatter.insert_space_after_closing_angle_bracket_in_type_parameters" value="insert"/>
@@ -162,6 +165,7 @@
 <setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_type_arguments" value="insert"/>
 <setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_type_parameters" value="insert"/>
 <setting id="org.eclipse.jdt.core.formatter.insert_space_after_ellipsis" value="insert"/>
+<setting id="org.eclipse.jdt.core.formatter.insert_space_after_lambda_arrow" value="insert"/>
 <setting id="org.eclipse.jdt.core.formatter.insert_space_after_opening_angle_bracket_in_parameterized_type_reference" value="do not insert"/>
 <setting id="org.eclipse.jdt.core.formatter.insert_space_after_opening_angle_bracket_in_type_arguments" value="do not insert"/>
 <setting id="org.eclipse.jdt.core.formatter.insert_space_after_opening_angle_bracket_in_type_parameters" value="do not insert"/>
@@ -187,6 +191,7 @@
 <setting id="org.eclipse.jdt.core.formatter.insert_space_after_question_in_conditional" value="insert"/>
 <setting id="org.eclipse.jdt.core.formatter.insert_space_after_question_in_wildcard" value="do not insert"/>
 <setting id="org.eclipse.jdt.core.formatter.insert_space_after_semicolon_in_for" value="insert"/>
+<setting id="org.eclipse.jdt.core.formatter.insert_space_after_semicolon_in_try_resources" value="insert"/>
 <setting id="org.eclipse.jdt.core.formatter.insert_space_after_unary_operator" value="do not insert"/>
 <setting id="org.eclipse.jdt.core.formatter.insert_space_before_and_in_type_parameter" value="insert"/>
 <setting id="org.eclipse.jdt.core.formatter.insert_space_before_assignment_operator" value="insert"/>
@@ -238,6 +243,7 @@
 <setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_type_arguments" value="do not insert"/>
 <setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_type_parameters" value="do not insert"/>
 <setting id="org.eclipse.jdt.core.formatter.insert_space_before_ellipsis" value="do not insert"/>
+<setting id="org.eclipse.jdt.core.formatter.insert_space_before_lambda_arrow" value="insert"/>
 <setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_angle_bracket_in_parameterized_type_reference" value="do not insert"/>
 <setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_angle_bracket_in_type_arguments" value="do not insert"/>
 <setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_angle_bracket_in_type_parameters" value="do not insert"/>
@@ -254,8 +260,8 @@
 <setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_bracket_in_array_allocation_expression" value="do not insert"/>
 <setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_bracket_in_array_reference" value="do not insert"/>
 <setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_bracket_in_array_type_reference" value="do not insert"/>
-<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_annotation_type_member_declaration" value="do not insert"/>
 <setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_annotation" value="do not insert"/>
+<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_annotation_type_member_declaration" value="do not insert"/>
 <setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_catch" value="insert"/>
 <setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_constructor_declaration" value="do not insert"/>
 <setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_enum_constant" value="do not insert"/>
@@ -274,8 +280,9 @@
 <setting id="org.eclipse.jdt.core.formatter.insert_space_before_prefix_operator" value="do not insert"/>
 <setting id="org.eclipse.jdt.core.formatter.insert_space_before_question_in_conditional" value="insert"/>
 <setting id="org.eclipse.jdt.core.formatter.insert_space_before_question_in_wildcard" value="do not insert"/>
-<setting id="org.eclipse.jdt.core.formatter.insert_space_before_semicolon_in_for" value="do not insert"/>
 <setting id="org.eclipse.jdt.core.formatter.insert_space_before_semicolon" value="do not insert"/>
+<setting id="org.eclipse.jdt.core.formatter.insert_space_before_semicolon_in_for" value="do not insert"/>
+<setting id="org.eclipse.jdt.core.formatter.insert_space_before_semicolon_in_try_resources" value="do not insert"/>
 <setting id="org.eclipse.jdt.core.formatter.insert_space_before_unary_operator" value="do not insert"/>
 <setting id="org.eclipse.jdt.core.formatter.insert_space_between_brackets_in_array_type_reference" value="do not insert"/>
 <setting id="org.eclipse.jdt.core.formatter.insert_space_between_empty_braces_in_array_initializer" value="do not insert"/>
@@ -302,6 +309,7 @@
 <setting id="org.eclipse.jdt.core.formatter.use_on_off_tags" value="true"/>
 <setting id="org.eclipse.jdt.core.formatter.use_tabs_only_for_leading_indentations" value="false"/>
 <setting id="org.eclipse.jdt.core.formatter.wrap_before_binary_operator" value="true"/>
+<setting id="org.eclipse.jdt.core.formatter.wrap_before_or_operator_multicatch" value="true"/>
 <setting id="org.eclipse.jdt.core.formatter.wrap_outer_expressions_when_nested" value="true"/>
 </profile>
 </profiles>

diff --git a/utils/eclipse/README b/utils/eclipse/README
new file mode 100644 (file)
index 0000000..e69de29