JAL-2360 code formatting only and if-else changed to switch

diff --git a/src/jalview/schemes/BuriedColourScheme.java b/src/jalview/schemes/BuriedColourScheme.java
index 3c68da0..4a850f0 100755 (executable)
--- a/src/jalview/schemes/BuriedColourScheme.java
+++ b/src/jalview/schemes/BuriedColourScheme.java
@@ -47,6 +47,7 @@ public class BuriedColourScheme extends ScoreColourScheme
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public Color makeColour(float c)
   {
     return new Color(0, (float) (1.0 - c), c);

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index ca4316f..33bd0d9 100755 (executable)
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -74,6 +74,7 @@ public class ClustalxColourScheme extends ResidueColourScheme
     alignmentChanged(alignment, hiddenReps);
   }
 
+  @Override
   public void alignmentChanged(AnnotatedCollectionI alignment,
           Map<SequenceI, SequenceCollectionI> hiddenReps)
   {

diff --git a/src/jalview/schemes/ColourSchemeI.java b/src/jalview/schemes/ColourSchemeI.java
index da99a4a..fb86888 100755 (executable)
--- a/src/jalview/schemes/ColourSchemeI.java
+++ b/src/jalview/schemes/ColourSchemeI.java
@@ -35,7 +35,7 @@ public interface ColourSchemeI
    * @param c
    * @return the colour for the given character
    */
-  public Color findColour(char c);
+  Color findColour(char c);
 
   /**
    * 
@@ -48,51 +48,51 @@ public interface ColourSchemeI
    * @return context dependent colour for the given symbol at the position in
    *         the given sequence
    */
-  public Color findColour(char c, int j, SequenceI seq);
+  Color findColour(char c, int j, SequenceI seq);
 
   /**
    * assign the given consensus profile for the colourscheme
    */
-  public void setConsensus(ProfilesI hconsensus);
+  void setConsensus(ProfilesI hconsensus);
 
   /**
    * assign the given conservation to the colourscheme
    * 
    * @param c
    */
-  public void setConservation(jalview.analysis.Conservation c);
+  void setConservation(jalview.analysis.Conservation c);
 
   /**
    * enable or disable conservation shading for this colourscheme
    * 
    * @param conservationApplied
    */
-  public void setConservationApplied(boolean conservationApplied);
+  void setConservationApplied(boolean conservationApplied);
 
   /**
    * 
    * @return true if conservation shading is enabled for this colourscheme
    */
-  public boolean conservationApplied();
+  boolean conservationApplied();
 
   /**
    * set scale factor for bleaching of colour in unconserved regions
    * 
    * @param i
    */
-  public void setConservationInc(int i);
+  void setConservationInc(int i);
 
   /**
    * 
    * @return scale factor for bleaching colour in unconserved regions
    */
-  public int getConservationInc();
+  int getConservationInc();
 
   /**
    * 
    * @return percentage identity threshold for applying colourscheme
    */
-  public int getThreshold();
+  int getThreshold();
 
   /**
    * set percentage identity threshold and type of %age identity calculation for
@@ -103,7 +103,7 @@ public interface ColourSchemeI
    * @param ignoreGaps
    *          when true, calculate PID without including gapped positions
    */
-  public void setThreshold(int ct, boolean ignoreGaps);
+  void setThreshold(int ct, boolean ignoreGaps);
 
   /**
    * recalculate dependent data using the given sequence collection, taking
@@ -112,7 +112,7 @@ public interface ColourSchemeI
    * @param alignment
    * @param hiddenReps
    */
-  public void alignmentChanged(AnnotatedCollectionI alignment,
+  void alignmentChanged(AnnotatedCollectionI alignment,
           Map<SequenceI, SequenceCollectionI> hiddenReps);
 
   /**
@@ -123,7 +123,6 @@ public interface ColourSchemeI
    * @param hiddenRepSequences
    * @return copy of current scheme with any inherited settings transfered
    */
-  public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+  ColourSchemeI applyTo(AnnotatedCollectionI sg,
           Map<SequenceI, SequenceCollectionI> hiddenRepSequences);
-
 }

diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index 0d9c39d..fc703ba 100755 (executable)
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@ -415,8 +415,7 @@ 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)
@@ -425,7 +424,7 @@ public class ColourSchemeProperty
         }
       }
     }
-    return getColour(alignment, getColourIndexFromName(name));
+    return getColour(alignment, colindex);
   }
 
   /**
@@ -538,61 +537,64 @@ public class ColourSchemeProperty
     return cs;
   }
 
+  /**
+   * Returns the Color constant for a given colour name e.g. "pink", or null if
+   * the name is not recognised
+   * 
+   * @param name
+   * @return
+   */
   public static Color getAWTColorFromName(String name)
   {
+    if (name == null)
+    {
+      return null;
+    }
     Color col = null;
     name = name.toLowerCase();
-    if (name.equals("black"))
+
+    // or make a static map; or use reflection on the field name
+    switch (name)
     {
+    case "black":
       col = Color.black;
-    }
-    else if (name.equals("blue"))
-    {
+      break;
+    case "blue":
       col = Color.blue;
-    }
-    else if (name.equals("cyan"))
-    {
+      break;
+    case "cyan":
       col = Color.cyan;
-    }
-    else if (name.equals("darkGray"))
-    {
+      break;
+    case "darkGray":
       col = Color.darkGray;
-    }
-    else if (name.equals("gray"))
-    {
+      break;
+    case "gray":
       col = Color.gray;
-    }
-    else if (name.equals("green"))
-    {
+      break;
+    case "green":
       col = Color.green;
-    }
-    else if (name.equals("lightGray"))
-    {
+      break;
+    case "lightGray":
       col = Color.lightGray;
-    }
-    else if (name.equals("magenta"))
-    {
+      break;
+    case "magenta":
       col = Color.magenta;
-    }
-    else if (name.equals("orange"))
-    {
+      break;
+    case "orange":
       col = Color.orange;
-    }
-    else if (name.equals("pink"))
-    {
+      break;
+    case "pink":
       col = Color.pink;
-    }
-    else if (name.equals("red"))
-    {
+      break;
+    case "red":
       col = Color.red;
-    }
-    else if (name.equals("white"))
-    {
+      break;
+    case "white":
       col = Color.white;
-    }
-    else if (name.equals("yellow"))
-    {
+      break;
+    case "yellow":
       col = Color.yellow;
+      break;
     }
 
     return col;

diff --git a/src/jalview/schemes/CovariationColourScheme.java b/src/jalview/schemes/CovariationColourScheme.java
index 49d5dee..4701e0b 100644 (file)
--- a/src/jalview/schemes/CovariationColourScheme.java
+++ b/src/jalview/schemes/CovariationColourScheme.java
@@ -85,6 +85,7 @@ public class CovariationColourScheme extends ResidueColourScheme
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public Color findColour(char c)
   {
     // System.out.println("called"); log.debug

diff --git a/src/jalview/schemes/HelixColourScheme.java b/src/jalview/schemes/HelixColourScheme.java
index 1242cd3..c6ac7a5 100755 (executable)
--- a/src/jalview/schemes/HelixColourScheme.java
+++ b/src/jalview/schemes/HelixColourScheme.java
@@ -30,6 +30,7 @@ public class HelixColourScheme extends ScoreColourScheme
             ResidueProperties.helixmin, ResidueProperties.helixmax);
   }
 
+  @Override
   public Color makeColour(float c)
   {
     return new Color(c, (float) 1.0 - c, c);

diff --git a/src/jalview/schemes/HydrophobicColourScheme.java b/src/jalview/schemes/HydrophobicColourScheme.java
index 055000f..954471f 100755 (executable)
--- a/src/jalview/schemes/HydrophobicColourScheme.java
+++ b/src/jalview/schemes/HydrophobicColourScheme.java
@@ -47,6 +47,7 @@ public class HydrophobicColourScheme extends ScoreColourScheme
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public Color makeColour(float c)
   {
     return new Color(c, (float) 0.0, (float) 1.0 - c);

diff --git a/src/jalview/schemes/PurinePyrimidineColourScheme.java b/src/jalview/schemes/PurinePyrimidineColourScheme.java
index d2b878d..8bbbd15 100644 (file)
--- a/src/jalview/schemes/PurinePyrimidineColourScheme.java
+++ b/src/jalview/schemes/PurinePyrimidineColourScheme.java
@@ -47,6 +47,7 @@ public class PurinePyrimidineColourScheme extends ResidueColourScheme
    * @return Color from purinepyrimidineIndex in
    *         jalview.schemes.ResidueProperties
    */
+  @Override
   public Color findColour(char c)
   {
     return colors[ResidueProperties.purinepyrimidineIndex[c]];

diff --git a/src/jalview/schemes/RNAInteractionColourScheme.java b/src/jalview/schemes/RNAInteractionColourScheme.java
index 794195a..db1401a 100644 (file)
--- a/src/jalview/schemes/RNAInteractionColourScheme.java
+++ b/src/jalview/schemes/RNAInteractionColourScheme.java
@@ -31,34 +31,17 @@ public class RNAInteractionColourScheme extends ResidueColourScheme
     super();
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param n
-   *          DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
   @Override
   public Color findColour(char c)
   {
-    // System.out.println("called"); log.debug
+    // FIXME this is just a copy of NucleotideColourScheme
     return colors[ResidueProperties.nucleotideIndex[c]];
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param n
-   *          DOCUMENT ME!
-   * @param j
-   *          DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
   @Override
   public Color findColour(char c, int j, SequenceI seq)
   {
+    // FIXME this is just a copy of NucleotideColourScheme
     Color currentColour;
     if ((threshold == 0) || aboveThreshold(c, j))
     {

diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index f6b7c5e..e675a27 100755 (executable)
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -34,10 +34,7 @@ import java.awt.Color;
 import java.util.Map;
 
 /**
- * DOCUMENT ME!
- * 
- * @author $author$
- * @version $Revision$
+ * Base class for residue-based colour schemes
  */
 public class ResidueColourScheme implements ColourSchemeI
 {

diff --git a/src/jalview/schemes/StrandColourScheme.java b/src/jalview/schemes/StrandColourScheme.java
index 1340de3..56a2d90 100755 (executable)
--- a/src/jalview/schemes/StrandColourScheme.java
+++ b/src/jalview/schemes/StrandColourScheme.java
@@ -47,6 +47,7 @@ public class StrandColourScheme extends ScoreColourScheme
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public Color makeColour(float c)
   {
     return new Color(c, c, (float) 1.0 - c);

diff --git a/src/jalview/schemes/TurnColourScheme.java b/src/jalview/schemes/TurnColourScheme.java
index 22422ff..2c95755 100755 (executable)
--- a/src/jalview/schemes/TurnColourScheme.java
+++ b/src/jalview/schemes/TurnColourScheme.java
@@ -47,6 +47,7 @@ public class TurnColourScheme extends ScoreColourScheme
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public Color makeColour(float c)
   {
     return new Color(c, 1 - c, 1 - c);