JAL-3210 Barebones gradle/buildship/eclipse. See README

[jalview.git] / src / jalview / schemes / FeatureColour.java

diff --git a/src/jalview/schemes/FeatureColour.java b/src/jalview/schemes/FeatureColour.java
index 55fdf24..0d36f4f 100644 (file)
--- a/src/jalview/schemes/FeatureColour.java
+++ b/src/jalview/schemes/FeatureColour.java
@@ -25,6 +25,7 @@ import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.features.FeatureMatcher;
 import jalview.util.ColorUtils;
 import jalview.util.Format;
+import jalview.util.MessageManager;
 
 import java.awt.Color;
 import java.util.StringTokenizer;
@@ -50,6 +51,12 @@ import java.util.StringTokenizer;
  */
 public class FeatureColour implements FeatureColourI
 {
+  private static final String I18N_LABEL = MessageManager
+          .getString("label.label");
+
+  private static final String I18N_SCORE = MessageManager
+          .getString("label.score");
+
   private static final String ABSOLUTE = "abso";
 
   private static final String ABOVE = "above";
@@ -316,19 +323,19 @@ public class FeatureColour implements FeatureColourI
       {
         if (minval.length() > 0)
         {
-          min = new Float(minval).floatValue();
+          min = Float.valueOf(minval).floatValue();
         }
       } catch (Exception e)
       {
         throw new IllegalArgumentException(
-                "Couldn't parse the minimum value for graduated colour ("
-                        + descriptor + ")");
+                "Couldn't parse the minimum value for graduated colour ('"
+                        + minval + "')");
       }
       try
       {
         if (maxval.length() > 0)
         {
-          max = new Float(maxval).floatValue();
+          max = Float.valueOf(maxval).floatValue();
         }
       } catch (Exception e)
       {
@@ -396,7 +403,7 @@ public class FeatureColour implements FeatureColourI
         {
           gcol.nextToken();
           tval = gcol.nextToken();
-          featureColour.setThreshold(new Float(tval).floatValue());
+          featureColour.setThreshold(Float.valueOf(tval).floatValue());
         } catch (Exception e)
         {
           System.err.println("Couldn't parse threshold value as a float: ("
@@ -672,9 +679,12 @@ public class FeatureColour implements FeatureColourI
 
   /**
    * Returns the colour for the given instance of the feature. This may be a
-   * simple colour, a colour generated from the feature description (if
-   * isColourByLabel()), or a colour derived from the feature score (if
-   * isGraduatedColour()).
+   * simple colour, a colour generated from the feature description or other
+   * attribute (if isColourByLabel()), or a colour derived from the feature
+   * score or other attribute (if isGraduatedColour()).
+   * <p>
+   * Answers null if feature score (or attribute) value lies outside a
+   * configured threshold.
    * 
    * @param feature
    * @return
@@ -884,4 +894,78 @@ public class FeatureColour implements FeatureColourI
     attributeName = name;
   }
 
+  @Override
+  public boolean isOutwithThreshold(SequenceFeature feature)
+  {
+    if (!isGraduatedColour())
+    {
+      return false;
+    }
+    float scr = feature.getScore();
+    if (attributeName != null)
+    {
+      try
+      {
+        String attVal = feature.getValueAsString(attributeName);
+        scr = Float.valueOf(attVal);
+      } catch (Throwable e)
+      {
+        scr = Float.NaN;
+      }
+    }
+    if (Float.isNaN(scr))
+    {
+      return false;
+    }
+
+    return ((isAboveThreshold() && scr <= threshold)
+            || (isBelowThreshold() && scr >= threshold));
+  }
+
+  @Override
+  public String getDescription()
+  {
+    if (isSimpleColour())
+    {
+      return "r=" + colour.getRed() + ",g=" + colour.getGreen() + ",b="
+              + colour.getBlue();
+    }
+    StringBuilder tt = new StringBuilder();
+    String by = null;
+
+    if (getAttributeName() != null)
+    {
+      by = FeatureMatcher.toAttributeDisplayName(getAttributeName());
+    }
+    else if (isColourByLabel())
+    {
+      by = I18N_LABEL;
+    }
+    else
+    {
+      by = I18N_SCORE;
+    }
+    tt.append(MessageManager.formatMessage("action.by_title_param", by));
+
+    /*
+     * add threshold if any
+     */
+    if (isAboveThreshold() || isBelowThreshold())
+    {
+      tt.append(" (");
+      if (isColourByLabel())
+      {
+        /*
+         * Jalview features file supports the combination of 
+         * colour by label or attribute text with score threshold
+         */
+        tt.append(I18N_SCORE).append(" ");
+      }
+      tt.append(isAboveThreshold() ? "> " : "< ");
+      tt.append(getThreshold()).append(")");
+    }
+
+    return tt.toString();
+  }
+
 }