Merge branch 'develop' into releases/Release_2_11_Branch

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

diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index e44c32d..d992e4e 100644 (file)
--- a/src/jalview/controller/AlignViewController.java
+++ b/src/jalview/controller/AlignViewController.java
@@ -53,20 +53,19 @@ public class AlignViewController implements AlignViewControllerI
   private AlignViewControllerGuiI avcg;
 
   public AlignViewController(AlignViewControllerGuiI alignFrame,
-          AlignViewportI viewport, AlignmentViewPanel alignPanel)
+          AlignViewportI vp, AlignmentViewPanel ap)
   {
     this.avcg = alignFrame;
-    this.viewport = viewport;
-    this.alignPanel = alignPanel;
+    this.viewport = vp;
+    this.alignPanel = ap;
   }
 
   @Override
-  public void setViewportAndAlignmentPanel(AlignViewportI viewport,
-          AlignmentViewPanel alignPanel)
+  public void setViewportAndAlignmentPanel(AlignViewportI vp,
+          AlignmentViewPanel ap)
   {
-    this.alignPanel = alignPanel;
-    this.viewport = viewport;
-
+    this.alignPanel = ap;
+    this.viewport = vp;
   }
 
   @Override
@@ -182,7 +181,7 @@ public class AlignViewController implements AlignViewControllerI
       if (changed)
       {
         viewport.setColumnSelection(cs);
-        alignPanel.paintAlignment(true);
+        alignPanel.paintAlignment(false, false);
         int columnCount = invert
                 ? (sqcol.getEndRes() - sqcol.getStartRes() + 1)
                         - bs.cardinality()
@@ -207,7 +206,7 @@ public class AlignViewController implements AlignViewControllerI
       if (!extendCurrent)
       {
         cs.clear();
-        alignPanel.paintAlignment(true);
+        alignPanel.paintAlignment(false, false);
       }
     }
     return false;
@@ -215,17 +214,21 @@ public class AlignViewController implements AlignViewControllerI
 
   /**
    * Sets a bit in the BitSet for each column (base 0) in the sequence
-   * collection which includes the specified feature type. Returns the number of
-   * sequences which have the feature in the selected range.
+   * collection which includes a visible feature of the specified feature type.
+   * Returns the number of sequences which have the feature visible in the
+   * selected range.
    * 
    * @param featureType
    * @param sqcol
    * @param bs
    * @return
    */
-  static int findColumnsWithFeature(String featureType,
+  int findColumnsWithFeature(String featureType,
           SequenceCollectionI sqcol, BitSet bs)
   {
+    FeatureRenderer fr = alignPanel == null ? null : alignPanel
+            .getFeatureRenderer();
+
     final int startColumn = sqcol.getStartRes() + 1; // converted to base 1
     final int endColumn = sqcol.getEndRes() + 1;
     List<SequenceI> seqs = sqcol.getSequences();
@@ -238,13 +241,19 @@ public class AlignViewController implements AlignViewControllerI
         List<SequenceFeature> sfs = sq.findFeatures(startColumn,
                 endColumn, featureType);
 
-        if (!sfs.isEmpty())
-        {
-          nseq++;
-        }
-
+        boolean found = false;
         for (SequenceFeature sf : sfs)
         {
+          if (fr.getColour(sf) == null)
+          {
+            continue;
+          }
+          if (!found)
+          {
+            nseq++;
+          }
+          found = true;
+
           int sfStartCol = sq.findIndex(sf.getBegin());
           int sfEndCol = sq.findIndex(sf.getEnd());
 
@@ -329,7 +338,7 @@ public class AlignViewController implements AlignViewControllerI
     AlignmentSorter.sortByFeature(typ, gps, start, stop, al, method);
     avcg.addHistoryItem(new OrderCommand(methodText, oldOrder,
             viewport.getAlignment()));
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, false);
 
   }
 
@@ -343,34 +352,34 @@ public class AlignViewController implements AlignViewControllerI
   public boolean parseFeaturesFile(String file, DataSourceType protocol,
           boolean relaxedIdMatching)
   {
-    boolean featuresFile = false;
+    boolean featuresAdded = false;
+    FeatureRenderer fr = alignPanel.getFeatureRenderer();
     try
     {
-      featuresFile = new FeaturesFile(false, file, protocol).parse(
-              viewport.getAlignment().getDataset(),
-              alignPanel.getFeatureRenderer().getFeatureColours(), false,
-              relaxedIdMatching);
+      featuresAdded = new FeaturesFile(false, file, protocol).parse(
+              viewport.getAlignment().getDataset(), fr.getFeatureColours(),
+              fr.getFeatureFilters(), false, relaxedIdMatching);
     } catch (Exception ex)
     {
       ex.printStackTrace();
     }
 
-    if (featuresFile)
+    if (featuresAdded)
     {
       avcg.refreshFeatureUI(true);
-      if (alignPanel.getFeatureRenderer() != null)
+      if (fr != null)
       {
         // update the min/max ranges where necessary
-        alignPanel.getFeatureRenderer().findAllFeatures(true);
+        fr.findAllFeatures(true);
       }
       if (avcg.getFeatureSettingsUI() != null)
       {
         avcg.getFeatureSettingsUI().discoverAllFeatureData();
       }
-      alignPanel.paintAlignment(true);
+      alignPanel.paintAlignment(true, true);
     }
 
-    return featuresFile;
+    return featuresAdded;
 
   }
 
@@ -406,7 +415,7 @@ public class AlignViewController implements AlignViewControllerI
       if (changed)
       {
         viewport.setColumnSelection(cs);
-        alignPanel.paintAlignment(true);
+        alignPanel.paintAlignment(false, false);
         int columnCount = invert
                 ? (sqcol.getEndRes() - sqcol.getStartRes() + 1)
                         - bs.cardinality()
@@ -430,7 +439,7 @@ public class AlignViewController implements AlignViewControllerI
       if (!extendCurrent)
       {
         cs.clear();
-        alignPanel.paintAlignment(true);
+        alignPanel.paintAlignment(false, false);
       }
     }
     return false;