Further abstractions and clean up

[jalview.git] / src / jalview / controller / AlignViewController.java

diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index 21cf630..7b42a30 100644 (file)
--- a/src/jalview/controller/AlignViewController.java
+++ b/src/jalview/controller/AlignViewController.java
@@ -20,11 +20,6 @@
  */
 package jalview.controller;
 
-import java.awt.Color;
-import java.util.ArrayList;
-import java.util.BitSet;
-import java.util.List;
-
 import jalview.analysis.AlignmentSorter;
 import jalview.api.AlignViewControllerGuiI;
 import jalview.api.AlignViewControllerI;
@@ -33,12 +28,20 @@ import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
 import jalview.commands.OrderCommand;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.util.MessageManager;
+import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
+import jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField;
+
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.BitSet;
+import java.util.List;
 
 public class AlignViewController implements AlignViewControllerI
 {
@@ -100,7 +103,9 @@ public class AlignViewController implements AlignViewControllerI
                 (int) (Math.random() * 255), (int) (Math.random() * 255));
         col = col.brighter();
         for (SequenceI sq : gps[g].getSequences(null))
+        {
           viewport.setSequenceColour(sq, col);
+        }
       }
       return true;
     }
@@ -300,6 +305,91 @@ public class AlignViewController implements AlignViewControllerI
     }
   }
 
+  public static boolean filterAnnotations(Annotation[] annotations,
+          AnnotationFilterParameter filterParams, ColumnSelection cs)
+  {
+    cs.revealAllHiddenColumns();
+    cs.clear();
+    int count = 0;
+    do
+    {
+      if (annotations[count] != null)
+      {
+
+        boolean itemMatched = false;
+
+        if (filterParams.getThresholdType() == AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD
+                && annotations[count].value > filterParams
+                        .getThresholdValue())
+        {
+          itemMatched = true;
+        }
+        if (filterParams.getThresholdType() == AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD
+                && annotations[count].value < filterParams
+                        .getThresholdValue())
+        {
+          itemMatched = true;
+        }
+
+        if (filterParams.isFilterAlphaHelix()
+                && annotations[count].secondaryStructure == 'H')
+        {
+          itemMatched = true;
+        }
+
+        if (filterParams.isFilterBetaSheet()
+                && annotations[count].secondaryStructure == 'E')
+        {
+          itemMatched = true;
+        }
+
+        if (filterParams.isFilterTurn()
+                && annotations[count].secondaryStructure == 'S')
+        {
+          itemMatched = true;
+        }
+
+        String regexSearchString = filterParams.getRegexString();
+        if (regexSearchString != null
+                && !filterParams.getRegexSearchFields().isEmpty())
+        {
+          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)
+          {
+            if (annotations[count].displayCharacter
+                    .equals(regexSearchString))
+            {
+              itemMatched = true;
+            }
+          }
+          if (fields.contains(SearchableAnnotationField.DESCRIPTION)
+                  && annotations[count].description != null
+                  && annotations[count].description
+                          .matches(regexSearchString))
+          {
+            itemMatched = true;
+          }
+        }
+
+        if (itemMatched)
+        {
+          cs.addElement(count);
+        }
+      }
+      count++;
+    } while (count < annotations.length);
+    return false;
+  }
+
   @Override
   public void sortAlignmentByFeatureDensity(String[] typ)
   {