Merge branch 'features/JAL-1541_BioJsMSAViewer-export-option' of https://source.jalvi...

Conflicts:
	src/jalview/gui/AlignViewport.java

diff --cc .externalToolBuilders/Jalview Release indices [Builder].launch
index 4c0c7dd,4c0c7dd..9d81cc8
--- 1/.externalToolBuilders/Jalview Release indices [Builder].launch
--- 2/.externalToolBuilders/Jalview Release indices [Builder].launch
+++ b/.externalToolBuilders/Jalview Release indices [Builder].launch
@@@ -14,6 -14,6 +14,7 @@@
  <stringAttribute key="org.eclipse.jdt.launching.CLASSPATH_PROVIDER" value="org.eclipse.ant.ui.AntClasspathProvider"/>
  <stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="jalview"/>
  <stringAttribute key="org.eclipse.jdt.launching.SOURCE_PATH_PROVIDER" value="org.eclipse.ant.ui.AntClasspathProvider"/>
++<stringAttribute key="org.eclipse.jdt.launching.VM_ARGUMENTS" value=""/>
  <stringAttribute key="org.eclipse.ui.externaltools.ATTR_ANT_TARGETS" value="buildindices,"/>
  <booleanAttribute key="org.eclipse.ui.externaltools.ATTR_BUILDER_ENABLED" value="true"/>
  <stringAttribute key="org.eclipse.ui.externaltools.ATTR_LAUNCH_CONFIGURATION_BUILD_SCOPE" value="${none}"/>

diff --cc .settings/org.eclipse.jdt.core.prefs
index 884491a,884491a..f72955b
--- 1/.settings/org.eclipse.jdt.core.prefs
--- 2/.settings/org.eclipse.jdt.core.prefs
+++ b/.settings/org.eclipse.jdt.core.prefs
@@@ -1,4 -1,4 +1,15 @@@
  eclipse.preferences.version=1
++org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
++org.eclipse.jdt.core.compiler.codegen.methodParameters=do not generate
++org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.7
++org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
++org.eclipse.jdt.core.compiler.compliance=1.7
++org.eclipse.jdt.core.compiler.debug.lineNumber=generate
++org.eclipse.jdt.core.compiler.debug.localVariable=generate
++org.eclipse.jdt.core.compiler.debug.sourceFile=generate
++org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
++org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
++org.eclipse.jdt.core.compiler.source=1.7
  org.eclipse.jdt.core.formatter.align_type_members_on_columns=false
  org.eclipse.jdt.core.formatter.alignment_for_arguments_in_allocation_expression=16
  org.eclipse.jdt.core.formatter.alignment_for_arguments_in_annotation=0

diff --cc src/jalview/gui/AlignFrame.java
Simple merge

diff --cc src/jalview/gui/AlignViewport.java
index 1a328f9,5c383d8..921189b
--- 1/src/jalview/gui/AlignViewport.java
--- 2/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@@ -1265,13 -1279,23 +1279,34 @@@ public class AlignViewport extends Alig
      }
    }
  
++<<<<<<< HEAD
 +  public Hashtable getFeaturesDisplayed()
 +  {
 +    return featuresDisplayed;
 +  }
 +
 +  public void setFeaturesDisplayed(Hashtable featuresDisplayed)
 +  {
 +    this.featuresDisplayed = featuresDisplayed;
++=======
+   protected SequenceAnnotationOrder getSortAnnotationsBy()
+   {
+     return sortAnnotationsBy;
+   }
+ 
+   protected void setSortAnnotationsBy(SequenceAnnotationOrder sortAnnotationsBy)
+   {
+     this.sortAnnotationsBy = sortAnnotationsBy;
+   }
+ 
+   protected boolean isShowAutocalculatedAbove()
+   {
+     return showAutocalculatedAbove;
+   }
+ 
+   protected void setShowAutocalculatedAbove(boolean showAutocalculatedAbove)
+   {
+     this.showAutocalculatedAbove = showAutocalculatedAbove;
++>>>>>>> branch 'features/JAL-1541_BioJsMSAViewer-export-option' of https://source.jalview.org/git/jalview.git
    }
  }