X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FColumnSelection.java;h=309aabfce991073fa492acc5a47826bc8d64c7a1;hb=eb7a26d5a2a6168aabe6a35d434aa6546159e977;hp=6d620b4a9cff66a9602fa900aace1809e983296d;hpb=3d0101179759ef157b088ea135423cd909512d9f;p=jalview.git

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index 6d620b4..309aabf 100644
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -20,13 +20,14 @@
  */
 package jalview.datamodel;
 
-import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
-import jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField;
-
 import java.util.ArrayList;
 import java.util.BitSet;
 import java.util.Collections;
 import java.util.List;
+import java.util.regex.PatternSyntaxException;
+
+import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
+import jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField;
 
 /**
  * Data class holding the selected columns and hidden column ranges for a view.
@@ -59,7 +60,7 @@ public class ColumnSelection
      */
     IntList()
     {
-      order = new ArrayList<Integer>();
+      order = new ArrayList<>();
       _uorder = Collections.unmodifiableList(order);
       selected = new BitSet();
     }
@@ -105,7 +106,7 @@ public class ColumnSelection
     void remove(int col)
     {
 
-      Integer colInt = new Integer(col);
+      Integer colInt = Integer.valueOf(col);
 
       if (selected.get(col))
       {
@@ -203,7 +204,7 @@ public class ColumnSelection
           // clear shifted bits and update List of selected columns
           selected.clear(temp);
           mask.set(temp - change);
-          order.set(i, new Integer(temp - change));
+          order.set(i, Integer.valueOf(temp - change));
         }
       }
       // lastly update the bitfield all at once
@@ -230,7 +231,7 @@ public class ColumnSelection
      */
     List<int[]> getRanges()
     {
-      List<int[]> rlist = new ArrayList<int[]>();
+      List<int[]> rlist = new ArrayList<>();
       if (selected.isEmpty())
       {
         return rlist;
@@ -263,7 +264,7 @@ public class ColumnSelection
     }
   }
 
-  IntList selection = new IntList();
+  private IntList selection = new IntList();
 
   /**
    * Add a column to the selection
@@ -308,7 +309,7 @@ public class ColumnSelection
     Integer colInt;
     for (int i = start; i < end; i++)
     {
-      colInt = new Integer(i);
+      colInt = Integer.valueOf(i);
       if (selection.contains(colInt))
       {
         selection.remove(colInt);
@@ -353,6 +354,22 @@ public class ColumnSelection
   }
 
   /**
+   * 
+   */
+  public boolean intersects(int from, int to)
+  {
+    // TODO: do this in a more efficient bitwise way
+    for (int f = from; f <= to; f++)
+    {
+      if (selection.isSelected(f))
+      {
+        return true;
+      }
+    }
+    return false;
+  }
+
+  /**
    * Answers true if no columns are selected, else false
    */
   public boolean isEmpty()
@@ -533,92 +550,124 @@ public class ColumnSelection
     return (selection != null && selection.size() > 0);
   }
 
-  public boolean filterAnnotations(Annotation[] annotations,
+  /**
+   * Selects columns where the given annotation matches the provided filter
+   * condition(s). Any existing column selections are first cleared. Answers the
+   * number of columns added.
+   * 
+   * @param annotations
+   * @param filterParams
+   * @return
+   */
+  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();
-    int count = 0;
+    int addedCount = 0;
+    int column = 0;
     do
     {
-      if (annotations[count] != null)
+      Annotation ann = annotations[column];
+      if (ann != null)
       {
-
-        boolean itemMatched = false;
+        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
-                && annotations[count].value >= filterParams
-                        .getThresholdValue())
+                && value > filterParams.getThresholdValue())
         {
-          itemMatched = true;
+          matched = true;
         }
-        if (filterParams
+
+        if (!matched && filterParams
                 .getThresholdType() == AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD
-                && annotations[count].value <= filterParams
-                        .getThresholdValue())
+                && value < filterParams.getThresholdValue())
         {
-          itemMatched = true;
+          matched = true;
         }
 
-        if (filterParams.isFilterAlphaHelix()
-                && annotations[count].secondaryStructure == 'H')
+        if (!matched && filterParams.isFilterAlphaHelix()
+                && ann.secondaryStructure == 'H')
         {
-          itemMatched = true;
+          matched = true;
         }
 
-        if (filterParams.isFilterBetaSheet()
-                && annotations[count].secondaryStructure == 'E')
+        if (!matched && filterParams.isFilterBetaSheet()
+                && ann.secondaryStructure == 'E')
         {
-          itemMatched = true;
+          matched = true;
         }
 
-        if (filterParams.isFilterTurn()
-                && annotations[count].secondaryStructure == 'S')
+        if (!matched && filterParams.isFilterTurn()
+                && ann.secondaryStructure == 'S')
         {
-          itemMatched = true;
+          matched = true;
         }
 
         String regexSearchString = filterParams.getRegexString();
-        if (regexSearchString != null
-                && !filterParams.getRegexSearchFields().isEmpty())
+        if (!matched && regexSearchString != null)
         {
           List<SearchableAnnotationField> fields = filterParams
                   .getRegexSearchFields();
-          try
-          {
-            if (fields.contains(SearchableAnnotationField.DISPLAY_STRING)
-                    && annotations[count].displayCharacter
-                            .matches(regexSearchString))
-            {
-              itemMatched = true;
-            }
-          } catch (java.util.regex.PatternSyntaxException pse)
+          for (SearchableAnnotationField field : fields)
           {
-            if (annotations[count].displayCharacter
-                    .equals(regexSearchString))
+            String compareTo = field == SearchableAnnotationField.DISPLAY_STRING
+                    ? ann.displayCharacter // match 'Label'
+                    : ann.description; // and/or 'Description'
+            if (compareTo != null)
             {
-              itemMatched = true;
+              try
+              {
+                if (compareTo.matches(regexSearchString))
+                {
+                  matched = true;
+                }
+              } catch (PatternSyntaxException pse)
+              {
+                if (compareTo.equals(regexSearchString))
+                {
+                  matched = true;
+                }
+              }
+              if (matched)
+              {
+                break;
+              }
             }
           }
-          if (fields.contains(SearchableAnnotationField.DESCRIPTION)
-                  && annotations[count].description != null
-                  && annotations[count].description
-                          .matches(regexSearchString))
-          {
-            itemMatched = true;
-          }
         }
 
-        if (itemMatched)
+        if (matched)
         {
-          this.addElement(count);
+          this.addElement(column);
+          addedCount++;
         }
       }
-      count++;
-    } while (count < annotations.length);
-    return false;
+      column++;
+    } while (column < annotations.length);
+
+    return addedCount;
   }
 
   /**