JAL-2016 first draft of pre-set feature colour scheme

diff --git a/src/jalview/api/FeatureColourI.java b/src/jalview/api/FeatureColourI.java
new file mode 100644 (file)
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--- /dev/null
+++ b/src/jalview/api/FeatureColourI.java
@@ -0,0 +1,82 @@
+package jalview.api;
+
+import java.awt.Color;
+
+public interface FeatureColourI
+{
+
+  /**
+   * Answers true when either isColourByLabel, isAboveThreshold or
+   * isBelowThreshold answers true
+   * 
+   * @return
+   */
+  boolean isGraduatedColour();
+
+  /**
+   * Returns the feature colour (when isGraduatedColour answers false)
+   * 
+   * @return
+   */
+  Color getColour();
+
+  /**
+   * Returns the minimum colour (when isGraduatedColour answers true)
+   * 
+   * @return
+   */
+  Color getMinColour();
+
+  /**
+   * Returns the maximum colour (when isGraduatedColour answers true)
+   * 
+   * @return
+   */
+  Color getMaxColour();
+
+  /**
+   * Answers true if the feature is coloured by label (description); only
+   * applicable when isGraduatedColour answers true
+   * 
+   * @return
+   */
+  boolean isColourByLabel();
+
+  /**
+   * Answers true if the feature is coloured below a threshold value; only
+   * applicable when isGraduatedColour answers true
+   * 
+   * @return
+   */
+  boolean isBelowThreshold();
+
+  /**
+   * Answers true if the feature is coloured above a threshold value; only
+   * applicable when isGraduatedColour answers true
+   * 
+   * @return
+   */
+  boolean isAboveThreshold();
+
+  /**
+   * Answers true if the threshold is the min (or max) of the colour range; only
+   * applicable when isGraduatedColour answers true
+   * 
+   * @return
+   */
+  boolean isThresholdMinMax();
+
+  /**
+   * Returns the threshold value (if any), else zero
+   * 
+   * @return
+   */
+  float getThreshold();
+
+  /**
+   * Answers true if ?
+   * 
+   * @return
+   */
+  boolean isLowToHigh();
+}

diff --git a/src/jalview/api/FeatureSettingsI.java b/src/jalview/api/FeatureSettingsI.java
new file mode 100644 (file)
index 0000000..55f52d2
--- /dev/null
+++ b/src/jalview/api/FeatureSettingsI.java
@@ -0,0 +1,66 @@
+package jalview.api;
+
+/**
+ * An interface that describes the settings configurable in the Feature Settings
+ * dialog.
+ * 
+ * @author gmcarstairs
+ *
+ */
+public interface FeatureSettingsI
+{
+  // note Java 8 will allow default implementations of these methods in the
+  // interface, simplifying instantiating classes
+
+  /**
+   * Answers true if the specified feature type is displayed
+   * 
+   * @param type
+   * @return
+   */
+  boolean isFeatureDisplayed(String type);
+
+  /**
+   * Answers true if the specified feature group is displayed
+   * 
+   * @param group
+   * @return
+   */
+  boolean isGroupDisplayed(String group);
+
+  /**
+   * Returns the colour (or graduated colour) for the feature type, or null if
+   * not known
+   * 
+   * @param type
+   * @return
+   */
+  FeatureColourI getFeatureColour(String type);
+
+  /**
+   * Returns the transparency value, from 0 (fully transparent) to 1 (fully
+   * opaque)
+   * 
+   * @return
+   */
+  float getTransparency();
+
+  /**
+   * Returns -1 if feature1 'precedes' (is displayed on top of) feature 2, +1 if
+   * feature2 is on top of feature1, or 0 if we don't care
+   * 
+   * @param feature1
+   * @param feature2
+   * @return
+   */
+  int compareTo(String feature1, String feature2);
+
+  /**
+   * Answers true if features should be initially sorted so that features with a
+   * shorter average length are displayed on top of those with a longer average
+   * length
+   * 
+   * @return
+   */
+  boolean optimiseOrder();
+}

diff --git a/src/jalview/schemes/FeatureColourAdapter.java b/src/jalview/schemes/FeatureColourAdapter.java
new file mode 100644 (file)
index 0000000..a86bee4
--- /dev/null
+++ b/src/jalview/schemes/FeatureColourAdapter.java
@@ -0,0 +1,73 @@
+package jalview.schemes;
+
+import jalview.api.FeatureColourI;
+
+import java.awt.Color;
+
+/**
+ * A convenience class with implementations of FeatureColourI methods. Override
+ * methods as required in subclasses.
+ */
+public class FeatureColourAdapter implements FeatureColourI
+{
+  @Override
+  public boolean isGraduatedColour()
+  {
+    return isColourByLabel() || isAboveThreshold() || isBelowThreshold();
+  }
+
+  @Override
+  public Color getColour()
+  {
+    return Color.BLACK;
+  }
+
+  @Override
+  public Color getMinColour()
+  {
+    return Color.WHITE;
+  }
+
+  @Override
+  public Color getMaxColour()
+  {
+    return Color.BLACK;
+  }
+
+  @Override
+  public boolean isColourByLabel()
+  {
+    return false;
+  }
+
+  @Override
+  public boolean isBelowThreshold()
+  {
+    return false;
+  }
+
+  @Override
+  public boolean isAboveThreshold()
+  {
+    return false;
+  }
+
+  @Override
+  public boolean isThresholdMinMax()
+  {
+    return false;
+  }
+
+  @Override
+  public float getThreshold()
+  {
+    return 0f;
+  }
+
+  @Override
+  public boolean isLowToHigh()
+  {
+    return true;
+  }
+
+}

diff --git a/src/jalview/schemes/FeatureColourScheme.java b/src/jalview/schemes/FeatureColourScheme.java
new file mode 100644 (file)
index 0000000..4a90b84
--- /dev/null
+++ b/src/jalview/schemes/FeatureColourScheme.java
@@ -0,0 +1,109 @@
+package jalview.schemes;
+
+import jalview.api.FeatureColourI;
+import jalview.api.FeatureSettingsI;
+
+import java.awt.Color;
+
+/**
+ * Pre-set configurations for feature settings
+ * 
+ * @author gmcarstairs
+ *
+ */
+public enum FeatureColourScheme implements FeatureSettingsI
+{
+  /**
+   * Show sequence variants in red, on top of exons coloured by label
+   */
+  EnsemblVariants
+  {
+
+    @Override
+    public boolean isFeatureDisplayed(String type)
+    {
+      // TODO accept SO sub-types of these features
+      // if (SequenceOntologyFactory.getInstance().isA(SequenceOntologyI.EXON...
+      return (EXON.equals(type) || SEQUENCE_VARIANT.equals(type));
+    }
+
+    @Override
+    public boolean isGroupDisplayed(String group)
+    {
+      return true;
+    }
+
+    @Override
+    public FeatureColourI getFeatureColour(String type)
+    {
+      if (EXON.equals(type))
+      {
+        return new FeatureColourAdapter()
+        {
+          @Override
+          public boolean isColourByLabel()
+          {
+            return true;
+          }
+        };
+      }
+      if (SEQUENCE_VARIANT.equals(type))
+      {
+        return new FeatureColourAdapter()
+        {
+
+          @Override
+          public Color getColour()
+          {
+            return Color.RED;
+          }
+        };
+      }
+      return null;
+    }
+
+    @Override
+    public float getTransparency()
+    {
+      return 1f;
+    }
+
+    /**
+     * Order sequence_variant above exon above the rest
+     */
+    @Override
+    public int compareTo(String feature1, String feature2)
+    {
+      if (SEQUENCE_VARIANT.equals(feature1))
+      {
+        return -1;
+      }
+      if (SEQUENCE_VARIANT.equals(feature2))
+      {
+        return +1;
+      }
+      if (EXON.equals(feature1))
+      {
+        return -1;
+      }
+      if (EXON.equals(feature2))
+      {
+        return +1;
+      }
+      return 0;
+    }
+
+    @Override
+    public boolean optimiseOrder()
+    {
+      return false;
+    };
+
+  };
+
+  // SequenceOntologyI.SEQUENCE_VARIANT
+  private static final String SEQUENCE_VARIANT = "sequence_variant";
+
+  // SequenceOntologyI.EXON
+  private static final String EXON = "exon";
+}