JAL-1807 explicit imports (jalview.schemes)

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index 121d6ca..b0822ca 100755 (executable)
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -27,6 +27,8 @@ import jalview.datamodel.Annotation;
 import jalview.datamodel.GraphLine;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
+import jalview.renderer.AnnotationRenderer;
+import jalview.util.Comparison;
 
 import java.awt.Color;
 import java.util.IdentityHashMap;
@@ -269,7 +271,7 @@ public class AnnotationColourGradient extends FollowerColourScheme
       if (annotation.annotations != null
               && j < annotation.annotations.length
               && annotation.annotations[j] != null
-              && !jalview.util.Comparison.isGap(c))
+              && !Comparison.isGap(c))
       {
         Annotation aj = annotation.annotations[j];
         // 'use original colours' => colourScheme != null
@@ -309,9 +311,9 @@ public class AnnotationColourGradient extends FollowerColourScheme
                 }
                 else
                 {
-                  currentColour = annotation.annotations[j].secondaryStructure == 'H' ? jalview.renderer.AnnotationRenderer.HELIX_COLOUR
-                          : annotation.annotations[j].secondaryStructure == 'E' ? jalview.renderer.AnnotationRenderer.SHEET_COLOUR
-                                  : jalview.renderer.AnnotationRenderer.STEM_COLOUR;
+                  currentColour = annotation.annotations[j].secondaryStructure == 'H' ? AnnotationRenderer.HELIX_COLOUR
+                          : annotation.annotations[j].secondaryStructure == 'E' ? AnnotationRenderer.SHEET_COLOUR
+                                  : AnnotationRenderer.STEM_COLOUR;
                 }
               }
             }

diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index 9d09259..d5d2924 100755 (executable)
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -24,6 +24,7 @@ import jalview.analysis.AAFrequency;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
 
 import java.awt.Color;
 import java.util.Map;
@@ -52,7 +53,7 @@ public class Blosum62ColourScheme extends ResidueColourScheme
 
     Color currentColour;
 
-    if (!jalview.util.Comparison.isGap(res))
+    if (!Comparison.isGap(res))
     {
       String max = (String) consensus[j].get(AAFrequency.MAXRESIDUE);
 

diff --git a/src/jalview/schemes/ColourSchemeI.java b/src/jalview/schemes/ColourSchemeI.java
index 1604da7..1589356 100755 (executable)
--- a/src/jalview/schemes/ColourSchemeI.java
+++ b/src/jalview/schemes/ColourSchemeI.java
@@ -20,15 +20,14 @@
  */
 package jalview.schemes;
 
-import java.awt.Color;
-import java.util.Map;
-
-import jalview.datamodel.AlignmentI;
+import jalview.analysis.Conservation;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
-import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 
+import java.awt.Color;
+import java.util.Map;
+
 public interface ColourSchemeI
 {
   /**
@@ -61,7 +60,7 @@ public interface ColourSchemeI
    * 
    * @param c
    */
-  public void setConservation(jalview.analysis.Conservation c);
+  public void setConservation(Conservation c);
 
   /**
    * enable or disable conservation shading for this colourscheme

diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index 5715ada..025a7a0 100755 (executable)
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@ -21,6 +21,7 @@
 package jalview.schemes;
 
 import jalview.datamodel.AnnotatedCollectionI;
+import jalview.util.ColorUtils;
 
 import java.awt.Color;
 
@@ -415,8 +416,7 @@ public class ColourSchemeProperty
         try
         {
           // fix the launchApp user defined coloursheme transfer bug
-          jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
-                  "white");
+          UserColourScheme ucs = new UserColourScheme("white");
           ucs.parseAppletParameter(name);
 
         } catch (Exception e)
@@ -442,8 +442,7 @@ public class ColourSchemeProperty
    * @return null or an instance of the colourscheme configured to colour given
    *         sequence set
    */
-  public static ColourSchemeI getColour(
-          jalview.datamodel.AnnotatedCollectionI coll, int index)
+  public static ColourSchemeI getColour(AnnotatedCollectionI coll, int index)
   {
     // TODO 3.0 2.8 refactor signature to take an alignmentI like container so
     // colourschemes based on annotation can be initialised
@@ -621,8 +620,7 @@ public class ColourSchemeProperty
     // Generate random colors and store
     for (; j <= n; j++)
     {
-      rnaHelices[j] = jalview.util.ColorUtils
-              .generateRandomColor(Color.white);
+      rnaHelices[j] = ColorUtils.generateRandomColor(Color.white);
     }
   }
 

diff --git a/src/jalview/schemes/CovariationColourScheme.java b/src/jalview/schemes/CovariationColourScheme.java
index 582faeb..48b7bee 100644 (file)
--- a/src/jalview/schemes/CovariationColourScheme.java
+++ b/src/jalview/schemes/CovariationColourScheme.java
@@ -20,10 +20,11 @@
  */
 package jalview.schemes;
 
-import java.awt.*;
-import java.util.Hashtable;
-
 import jalview.datamodel.AlignmentAnnotation;
+import jalview.util.ColorUtils;
+
+import java.awt.Color;
+import java.util.Hashtable;
 
 /**
  * Became RNAHelicesColour.java. Placeholder for true covariation color scheme
@@ -72,7 +73,7 @@ public class CovariationColourScheme extends ResidueColourScheme
     for (int j = 0; j <= numHelix; j++)
     {
       helixcolorhash.put(Integer.toString(j),
-              jalview.util.ColorUtils.generateRandomColor(Color.white));
+              ColorUtils.generateRandomColor(Color.white));
     }
 
   }

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index 9dd763d..c59d579 100755 (executable)
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -23,6 +23,7 @@ package jalview.schemes;
 import jalview.analysis.AAFrequency;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
 
 import java.awt.Color;
 
@@ -73,7 +74,7 @@ public class PIDColourScheme extends ResidueColourScheme
     {
       sc = ((Float) consensus[j].get(ignoreGaps)).floatValue();
 
-      if (!jalview.util.Comparison.isGap(c))
+      if (!Comparison.isGap(c))
       {
         for (int i = 0; i < thresholds.length; i++)
         {

diff --git a/src/jalview/schemes/PurinePyrimidineColourScheme.java b/src/jalview/schemes/PurinePyrimidineColourScheme.java
index 9c43ed1..3d08060 100644 (file)
--- a/src/jalview/schemes/PurinePyrimidineColourScheme.java
+++ b/src/jalview/schemes/PurinePyrimidineColourScheme.java
@@ -45,7 +45,7 @@ public class PurinePyrimidineColourScheme extends ResidueColourScheme
    *          Character in sequence
    * 
    * @return Color from purinepyrimidineIndex in
-   *         jalview.schemes.ResidueProperties
+   *         ResidueProperties
    */
   public Color findColour(char c)
   {

diff --git a/src/jalview/schemes/RNAHelicesColour.java b/src/jalview/schemes/RNAHelicesColour.java
index 57fcba5..be28d91 100644 (file)
--- a/src/jalview/schemes/RNAHelicesColour.java
+++ b/src/jalview/schemes/RNAHelicesColour.java
@@ -20,14 +20,15 @@
  */
 package jalview.schemes;
 
-import java.awt.*;
-import java.util.Hashtable;
-import java.util.Map;
-
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
+import jalview.util.ColorUtils;
+
+import java.awt.Color;
+import java.util.Hashtable;
+import java.util.Map;
 
 /**
  * Looks at the information computed from an RNA Stockholm format file on the
@@ -143,7 +144,7 @@ public class RNAHelicesColour extends ResidueColourScheme
         if (!helixcolorhash.containsKey(Integer.toString(j)))
         {
           helixcolorhash.put(Integer.toString(j),
-                  jalview.util.ColorUtils.generateRandomColor(Color.white));
+                  ColorUtils.generateRandomColor(Color.white));
         }
       }
     }
@@ -151,7 +152,7 @@ public class RNAHelicesColour extends ResidueColourScheme
 
   /**
    * Returns default color base on purinepyrimidineIndex in
-   * jalview.schemes.ResidueProperties (Allows coloring in sequence logo)
+   * ResidueProperties (Allows coloring in sequence logo)
    * 
    * @param c
    *          Character in sequence

diff --git a/src/jalview/schemes/RNAHelicesColourChooser.java b/src/jalview/schemes/RNAHelicesColourChooser.java
index ee9792a..99403ab 100644 (file)
--- a/src/jalview/schemes/RNAHelicesColourChooser.java
+++ b/src/jalview/schemes/RNAHelicesColourChooser.java
@@ -46,7 +46,7 @@ public class RNAHelicesColourChooser
 
   Hashtable oldgroupColours;
 
-  jalview.datamodel.AlignmentAnnotation currentAnnotation;
+  AlignmentAnnotation currentAnnotation;
 
   boolean adjusting = false;
 

diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index e3118ad..5294006 100755 (executable)
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -25,6 +25,7 @@ import jalview.analysis.Conservation;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
 import jalview.util.MessageManager;
 
 import java.awt.Color;
@@ -268,7 +269,7 @@ public class ResidueColourScheme implements ColourSchemeI
     if ((conservationLength > i) && (conservation[i] != '*')
             && (conservation[i] != '+'))
     {
-      if (jalview.util.Comparison.isGap(conservation[i]))
+      if (Comparison.isGap(conservation[i]))
       {
         currentColour = Color.white;
       }

diff --git a/src/jalview/schemes/ScoreColourScheme.java b/src/jalview/schemes/ScoreColourScheme.java
index 7eb920d..beb7b59 100755 (executable)
--- a/src/jalview/schemes/ScoreColourScheme.java
+++ b/src/jalview/schemes/ScoreColourScheme.java
@@ -21,6 +21,7 @@
 package jalview.schemes;
 
 import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
 
 import java.awt.Color;
 
@@ -102,7 +103,7 @@ public class ScoreColourScheme extends ResidueColourScheme
       }
     }
 
-    if (jalview.util.Comparison.isGap(c))
+    if (Comparison.isGap(c))
     {
       return Color.white;
     }