JAL-2349 JAL-3855 experimenting with filtering columns based on mean of contact map...

diff --git a/src/jalview/appletgui/AnnotationColumnChooser.java b/src/jalview/appletgui/AnnotationColumnChooser.java
index 206b132..37b45f9 100644 (file)
--- a/src/jalview/appletgui/AnnotationColumnChooser.java
+++ b/src/jalview/appletgui/AnnotationColumnChooser.java
@@ -20,12 +20,6 @@
  */
 package jalview.appletgui;
 
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.HiddenColumns;
-import jalview.schemes.AnnotationColourGradient;
-import jalview.util.MessageManager;
-import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
-
 import java.awt.BorderLayout;
 import java.awt.CardLayout;
 import java.awt.Checkbox;
@@ -48,6 +42,12 @@ import java.awt.event.TextEvent;
 import java.awt.event.TextListener;
 import java.util.Vector;
 
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.HiddenColumns;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.util.MessageManager;
+import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
+
 //import javax.swing.JPanel;
 
 //import net.miginfocom.swing.MigLayout;
@@ -492,8 +492,8 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     // filterAnnotations, because showing hidden columns has the side effect of
     // adding them to the selection
     av.showAllHiddenColumns();
-    av.getColumnSelection().filterAnnotations(
-            getCurrentAnnotation().annotations, filterParams);
+    av.getColumnSelection().filterAnnotations(getCurrentAnnotation(),
+            filterParams);
 
     if (getActionOption() == ACTION_OPTION_HIDE)
     {

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index 140a366..309aabf 100644 (file)
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -559,9 +559,10 @@ public class ColumnSelection
    * @param filterParams
    * @return
    */
-  public int filterAnnotations(Annotation[] annotations,
+  public int filterAnnotations(AlignmentAnnotation ann_row,
           AnnotationFilterParameter filterParams)
   {
+    Annotation[] annotations = ann_row.annotations;
     // JBPNote - this method needs to be refactored to become independent of
     // viewmodel package
     this.clear();
@@ -572,22 +573,36 @@ public class ColumnSelection
       Annotation ann = annotations[column];
       if (ann != null)
       {
+        float value = ann.value;
         boolean matched = false;
 
         /*
          * filter may have multiple conditions - 
          * these are or'd until a match is found
          */
+        if (ann_row.graph == AlignmentAnnotation.CUSTOMRENDERER)
+        {
+          if (ann_row.sequenceRef != null)
+          {
+            int cpos = ann_row.sequenceRef.findPosition(column) - 1;
+            ContactListI clist = ann_row.sequenceRef
+                    .getContactListFor(ann_row, cpos);
+            ContactRange crange = clist.getRangeFor(0,
+                    clist.getContactHeight());
+            value = (float) crange.getMean();
+          }
+        }
+
         if (filterParams
                 .getThresholdType() == AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD
-                && ann.value > filterParams.getThresholdValue())
+                && value > filterParams.getThresholdValue())
         {
           matched = true;
         }
 
         if (!matched && filterParams
                 .getThresholdType() == AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD
-                && ann.value < filterParams.getThresholdValue())
+                && value < filterParams.getThresholdValue())
         {
           matched = true;
         }

diff --git a/src/jalview/gui/AnnotationColumnChooser.java b/src/jalview/gui/AnnotationColumnChooser.java
index c0d4708..0b1ad93 100644 (file)
--- a/src/jalview/gui/AnnotationColumnChooser.java
+++ b/src/jalview/gui/AnnotationColumnChooser.java
@@ -21,14 +21,6 @@
 
 package jalview.gui;
 
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.HiddenColumns;
-import jalview.io.cache.JvCacheableInputBox;
-import jalview.schemes.AnnotationColourGradient;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
-
 import java.awt.BorderLayout;
 import java.awt.CardLayout;
 import java.awt.Color;
@@ -50,6 +42,13 @@ import javax.swing.JPanel;
 import javax.swing.JRadioButton;
 import javax.swing.border.TitledBorder;
 
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.HiddenColumns;
+import jalview.io.cache.JvCacheableInputBox;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
 import net.miginfocom.swing.MigLayout;
 
 @SuppressWarnings("serial")
@@ -376,7 +375,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter
     // filterAnnotations, because showing hidden columns has the side effect of
     // adding them to the selection
     av.showAllHiddenColumns();
-    av.getColumnSelection().filterAnnotations(currentAnnotation.annotations,
+    av.getColumnSelection().filterAnnotations(currentAnnotation,
             filterParams);
 
     boolean hideCols = getActionOption() == ACTION_OPTION_HIDE;

diff --git a/test/jalview/datamodel/ColumnSelectionTest.java b/test/jalview/datamodel/ColumnSelectionTest.java
index d581345..5cb8cf5 100644 (file)
--- a/test/jalview/datamodel/ColumnSelectionTest.java
+++ b/test/jalview/datamodel/ColumnSelectionTest.java
@@ -25,12 +25,6 @@ import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertTrue;
 import static org.testng.AssertJUnit.fail;
 
-import jalview.analysis.AlignmentGenerator;
-import jalview.gui.JvOptionPane;
-import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
-import jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField;
-import jalview.viewmodel.annotationfilter.AnnotationFilterParameter.ThresholdType;
-
 import java.util.Arrays;
 import java.util.BitSet;
 import java.util.Collections;
@@ -41,6 +35,12 @@ import java.util.List;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
+import jalview.analysis.AlignmentGenerator;
+import jalview.gui.JvOptionPane;
+import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
+import jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField;
+import jalview.viewmodel.annotationfilter.AnnotationFilterParameter.ThresholdType;
+
 public class ColumnSelectionTest
 {
 
@@ -606,6 +606,8 @@ public class ColumnSelectionTest
   public void testFilterAnnotations()
   {
     ColumnSelection cs = new ColumnSelection();
+    AlignmentAnnotation alann = new AlignmentAnnotation("dummy",
+            "dummyDesc", null);
 
     /*
      * filter with no conditions clears the selection
@@ -613,7 +615,8 @@ public class ColumnSelectionTest
     Annotation[] anns = new Annotation[] { null };
     AnnotationFilterParameter filter = new AnnotationFilterParameter();
     cs.addElement(3);
-    int added = cs.filterAnnotations(anns, filter);
+    alann.annotations = anns;
+    int added = cs.filterAnnotations(alann, filter);
     assertEquals(0, added);
     assertTrue(cs.isEmpty());
 
@@ -624,8 +627,8 @@ public class ColumnSelectionTest
     filter.addRegexSearchField(SearchableAnnotationField.DESCRIPTION);
     Annotation helix = new Annotation("(", "hello", '<', 2f);
     Annotation sheet = new Annotation("(", "world", '<', 2f);
-    added = cs.filterAnnotations(new Annotation[] { null, helix, sheet },
-            filter);
+    alann.annotations = new Annotation[] { null, helix, sheet };
+    added = cs.filterAnnotations(alann, filter);
     assertEquals(1, added);
     assertTrue(cs.contains(2));
 
@@ -635,8 +638,8 @@ public class ColumnSelectionTest
     filter = new AnnotationFilterParameter();
     filter.setRegexString("(");
     filter.addRegexSearchField(SearchableAnnotationField.DISPLAY_STRING);
-    added = cs.filterAnnotations(new Annotation[] { null, helix, sheet },
-            filter);
+    alann.annotations = new Annotation[] { null, helix, sheet };
+    added = cs.filterAnnotations(alann, filter);
     assertEquals(2, added);
     assertTrue(cs.contains(1));
     assertTrue(cs.contains(2));
@@ -650,9 +653,8 @@ public class ColumnSelectionTest
     sheet = new Annotation("x", "desc", 'E', 1f);
     Annotation turn = new Annotation("x", "desc", 'S', 2f);
     Annotation ann4 = new Annotation("x", "desc", 'Y', 3f);
-    added = cs
-            .filterAnnotations(new Annotation[]
-            { null, helix, sheet, turn, ann4 }, filter);
+    alann.annotations = new Annotation[] { null, helix, sheet, turn, ann4 };
+    added = cs.filterAnnotations(alann, filter);
     assertEquals(1, added);
     assertTrue(cs.contains(1));
 
@@ -660,9 +662,8 @@ public class ColumnSelectionTest
      * select Helix and Sheet (E)
      */
     filter.setFilterBetaSheet(true);
-    added = cs
-            .filterAnnotations(new Annotation[]
-            { null, helix, sheet, turn, ann4 }, filter);
+    alann.annotations = new Annotation[] { null, helix, sheet, turn, ann4 };
+    added = cs.filterAnnotations(alann, filter);
     assertEquals(2, added);
     assertTrue(cs.contains(1));
     assertTrue(cs.contains(2));
@@ -672,9 +673,8 @@ public class ColumnSelectionTest
      */
     filter.setFilterAlphaHelix(false);
     filter.setFilterTurn(true);
-    added = cs
-            .filterAnnotations(new Annotation[]
-            { null, helix, sheet, turn, ann4 }, filter);
+    alann.annotations = new Annotation[] { null, helix, sheet, turn, ann4 };
+    added = cs.filterAnnotations(alann, filter);
     assertEquals(2, added);
     assertTrue(cs.contains(2));
     assertTrue(cs.contains(3));
@@ -685,9 +685,8 @@ public class ColumnSelectionTest
     filter = new AnnotationFilterParameter();
     filter.setThresholdType(ThresholdType.BELOW_THRESHOLD);
     filter.setThresholdValue(2f);
-    added = cs
-            .filterAnnotations(new Annotation[]
-            { null, helix, sheet, turn, ann4 }, filter);
+    alann.annotations = new Annotation[] { null, helix, sheet, turn, ann4 };
+    added = cs.filterAnnotations(alann, filter);
     assertEquals(2, added);
     assertTrue(cs.contains(1));
     assertTrue(cs.contains(2));
@@ -696,9 +695,8 @@ public class ColumnSelectionTest
      * select value > 2f (ann4 only)
      */
     filter.setThresholdType(ThresholdType.ABOVE_THRESHOLD);
-    added = cs
-            .filterAnnotations(new Annotation[]
-            { null, helix, sheet, turn, ann4 }, filter);
+    alann.annotations = new Annotation[] { null, helix, sheet, turn, ann4 };
+    added = cs.filterAnnotations(alann, filter);
     assertEquals(1, added);
     assertTrue(cs.contains(4));
 
@@ -706,9 +704,8 @@ public class ColumnSelectionTest
      * select >2f or Helix
      */
     filter.setFilterAlphaHelix(true);
-    added = cs
-            .filterAnnotations(new Annotation[]
-            { null, helix, sheet, turn, ann4 }, filter);
+    alann.annotations = new Annotation[] { null, helix, sheet, turn, ann4 };
+    added = cs.filterAnnotations(alann, filter);
     assertEquals(2, added);
     assertTrue(cs.contains(1));
     assertTrue(cs.contains(4));
@@ -719,9 +716,8 @@ public class ColumnSelectionTest
      */
     filter.setThresholdType(ThresholdType.BELOW_THRESHOLD);
     filter.setThresholdValue(1f);
-    added = cs
-            .filterAnnotations(new Annotation[]
-            { null, helix, sheet, turn, ann4 }, filter);
+    alann.annotations = new Annotation[] { null, helix, sheet, turn, ann4 };
+    added = cs.filterAnnotations(alann, filter);
     assertEquals(1, added);
     assertTrue(cs.contains(1));
   }