JAL-1553 enhancement of column selection by annotation row to include the query filte...

[jalview.git] / src / jalview / gui / AnnotationRowFilter.java

diff --git a/src/jalview/gui/AnnotationRowFilter.java b/src/jalview/gui/AnnotationRowFilter.java
index 9e205c4..ed59ef6 100644 (file)
--- a/src/jalview/gui/AnnotationRowFilter.java
+++ b/src/jalview/gui/AnnotationRowFilter.java
@@ -3,6 +3,8 @@ package jalview.gui;
 import jalview.api.AnnotationRowFilterI;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.AnnotationFilterParameter;
+import jalview.datamodel.AnnotationFilterParameter.SearchableAnnotationField;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.GraphLine;
 import jalview.datamodel.SequenceGroup;
@@ -12,6 +14,7 @@ import jalview.util.MessageManager;
 import java.awt.event.ActionEvent;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
+import java.util.List;
 import java.util.Vector;
 
 import javax.swing.JCheckBox;
@@ -156,7 +159,6 @@ public abstract class AnnotationRowFilter extends JPanel implements
         }
       }
     }
-    // seqAssociated.setEnabled(enableSeqAss);
     this.annmap = new int[list.size()];
     System.arraycopy(anmap, 0, this.annmap, 0, this.annmap.length);
     return list;
@@ -364,76 +366,87 @@ public abstract class AnnotationRowFilter extends JPanel implements
     return false;
   }
 
-  protected boolean markColumnsContaining(
-          AlignmentAnnotation currentAnnotation, int thresholdComparisonType)
+  protected boolean filterAnnotations(Annotation[] annotations,
+          AnnotationFilterParameter filterParams, ColumnSelection cs)
   {
-    try
+    av.showAllHiddenColumns();
+    cs.clear();
+    int count = 0;
+    do
     {
-      if (currentAnnotation != null)
+      if (annotations[count] != null)
       {
-        Annotation[] annotations = currentAnnotation.annotations;
-        ColumnSelection cs = av.getColumnSelection();
-        cs.clear();
-        if (thresholdComparisonType == AnnotationColourGradient.NO_THRESHOLD)
+
+        boolean itemMatched = false;
+
+        if (filterParams.getThresholdType() == AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD
+                && annotations[count].value > currentAnnotation.threshold.value)
         {
-          int count = 0;
-          do
-          {
-            if (annotations[count] != null)
-            {
-              if (currentAnnotation.label.equals("Secondary Structure")
-                      && annotations[count].secondaryStructure != ' ')
-              {
-                cs.addElement(count);
-              }
-              else if (currentAnnotation.label
-                      .equals("Iron Sulphur Contacts"))
-              {
-                cs.addElement(count);
-              }
-              else if (annotations[count].value != 0.0)
-              {
-                cs.addElement(count);
-              }
+          itemMatched = true;
+        }
+        if (filterParams.getThresholdType() == AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD
+                && annotations[count].value < currentAnnotation.threshold.value)
+        {
+          itemMatched = true;
+        }
 
-            }
-            count++;
-          } while (count < annotations.length);
+        if (filterParams.isFilterAlphaHelix()
+                && annotations[count].secondaryStructure == 'H')
+        {
+          itemMatched = true;
         }
-        else
+
+        if (filterParams.isFilterBetaSheet()
+                && annotations[count].secondaryStructure == 'E')
+        {
+          itemMatched = true;
+        }
+
+        if (filterParams.isFilterTurn()
+                && annotations[count].secondaryStructure == 'S')
         {
-          int count = 0;
-          do
+          itemMatched = true;
+        }
+
+        String regexSearchString = filterParams.getRegexString();
+        if (regexSearchString != null
+                && !filterParams.getRegexSearchFields().isEmpty())
+        {
+          List<SearchableAnnotationField> fields = filterParams
+                  .getRegexSearchFields();
+          try
           {
-            if (annotations[count] != null)
+            if (fields.contains(SearchableAnnotationField.DISPLAY_STRING)
+                    && annotations[count].displayCharacter
+                            .matches(regexSearchString))
             {
-              if (thresholdComparisonType == AnnotationColourGradient.ABOVE_THRESHOLD)
-              {
-                if (annotations[count].value > currentAnnotation.threshold.value)
-                {
-                  cs.addElement(count);
-                }
-              }
-              else if (thresholdComparisonType == AnnotationColourGradient.BELOW_THRESHOLD)
-              {
-                if (annotations[count].value < currentAnnotation.threshold.value)
-                {
-                  cs.addElement(count);
-                }
-              }
-
+              itemMatched = true;
             }
-            count++;
-          } while (count < annotations.length);
+          } 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;
+          }
         }
-      }
 
-      return true;
-    } catch (Exception e)
-    {
-      e.printStackTrace();
-      return false;
-    }
+        if (itemMatched)
+        {
+          cs.addElement(count);
+        }
+      }
+      count++;
+    } while (count < annotations.length);
+    return false;
   }
 
   public jalview.datamodel.AlignmentAnnotation getCurrentAnnotation()