JAL-3148 SequenceRenderer interface renamed SequenceRendererI

diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index e55f2a5..907d29e 100755 (executable)
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -30,7 +30,7 @@ import java.awt.Font;
 import java.awt.FontMetrics;
 import java.awt.Graphics;
 
-public class SequenceRenderer implements jalview.api.SequenceRenderer
+public class SequenceRenderer implements jalview.api.SequenceRendererI
 {
   final static int CHAR_TO_UPPER = 'A' - 'a';
 

diff --git a/src/jalview/ext/jmol/JmolCommands.java b/src/jalview/ext/jmol/JmolCommands.java
index 8fb0de6..b2aeee4 100644 (file)
--- a/src/jalview/ext/jmol/JmolCommands.java
+++ b/src/jalview/ext/jmol/JmolCommands.java
@@ -23,7 +23,7 @@ package jalview.ext.jmol;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
-import jalview.api.SequenceRenderer;
+import jalview.api.SequenceRendererI;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SequenceI;
@@ -55,7 +55,7 @@ public class JmolCommands
    */
   public static StructureMappingcommandSet[] getColourBySequenceCommand(
           StructureSelectionManager ssm, String[] files,
-          SequenceI[][] sequence, SequenceRenderer sr,
+          SequenceI[][] sequence, SequenceRendererI sr,
           AlignmentViewPanel viewPanel)
   {
     FeatureRenderer fr = viewPanel.getFeatureRenderer();
@@ -69,8 +69,7 @@ public class JmolCommands
     {
       StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
       StringBuffer command = new StringBuffer();
-      StructureMappingcommandSet smc;
-      ArrayList<String> str = new ArrayList<String>();
+      List<String> str = new ArrayList<>();
 
       if (mapping == null || mapping.length < 1)
       {

diff --git a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
index dad8511..f952bff 100644 (file)
--- a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
+++ b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
@@ -23,7 +23,7 @@ package jalview.ext.rbvi.chimera;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
-import jalview.api.SequenceRenderer;
+import jalview.api.SequenceRendererI;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SequenceFeature;
@@ -66,7 +66,7 @@ public class ChimeraCommands
    */
   public static StructureMappingcommandSet[] getColourBySequenceCommand(
           StructureSelectionManager ssm, String[] files,
-          SequenceI[][] sequence, SequenceRenderer sr,
+          SequenceI[][] sequence, SequenceRendererI sr,
           AlignmentViewPanel viewPanel)
   {
     Map<Object, AtomSpecModel> colourMap = buildColoursMap(ssm, files,
@@ -188,7 +188,7 @@ public class ChimeraCommands
    */
   protected static Map<Object, AtomSpecModel> buildColoursMap(
           StructureSelectionManager ssm, String[] files,
-          SequenceI[][] sequence, SequenceRenderer sr,
+          SequenceI[][] sequence, SequenceRendererI sr,
           AlignmentViewPanel viewPanel)
   {
     FeatureRenderer fr = viewPanel.getFeatureRenderer();

diff --git a/src/jalview/ext/varna/VarnaCommands.java b/src/jalview/ext/varna/VarnaCommands.java
index 4dd0648..e0524e8 100644 (file)
--- a/src/jalview/ext/varna/VarnaCommands.java
+++ b/src/jalview/ext/varna/VarnaCommands.java
@@ -20,7 +20,7 @@
  */
 package jalview.ext.varna;
 
-import jalview.api.SequenceRenderer;
+import jalview.api.SequenceRendererI;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
 import jalview.renderer.seqfeatures.FeatureColourFinder;
@@ -47,7 +47,7 @@ public class VarnaCommands
    */
   public static String[] getColourBySequenceCommand(
           StructureSelectionManager ssm, String[] files,
-          SequenceI[][] sequence, SequenceRenderer sr,
+          SequenceI[][] sequence, SequenceRendererI sr,
           FeatureColourFinder finder, AlignmentI alignment)
   {
     ArrayList<String> str = new ArrayList<String>();

diff --git a/src/jalview/javascript/MouseOverStructureListener.java b/src/jalview/javascript/MouseOverStructureListener.java
index 6071933..fd2a4d5 100644 (file)
--- a/src/jalview/javascript/MouseOverStructureListener.java
+++ b/src/jalview/javascript/MouseOverStructureListener.java
@@ -22,7 +22,7 @@ package jalview.javascript;
 
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
-import jalview.api.SequenceRenderer;
+import jalview.api.SequenceRendererI;
 import jalview.appletgui.AlignFrame;
 import jalview.bin.JalviewLite;
 import jalview.datamodel.SequenceI;
@@ -203,7 +203,7 @@ public class MouseOverStructureListener extends JSFunctionExec
         // }
       }
 
-      SequenceRenderer sr = ((jalview.appletgui.AlignmentPanel) source)
+      SequenceRendererI sr = ((jalview.appletgui.AlignmentPanel) source)
               .getSequenceRenderer();
       FeatureRenderer fr = ((jalview.appletgui.AlignmentPanel) source).av
               .isShowSequenceFeatures()