Merge branch 'features/JAL-4071_visibleFeaturesCounter' into features/JAL-3417_sdppre...

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

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 5366913..9280fb1 100644 (file)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -20,30 +20,6 @@
  */
 package jalview.gui;
 
-import jalview.analysis.AnnotationSorter;
-import jalview.api.AlignViewportI;
-import jalview.api.AlignmentViewPanel;
-import jalview.bin.Cache;
-import jalview.bin.Console;
-import jalview.bin.Jalview;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.HiddenColumns;
-import jalview.datamodel.SearchResultsI;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.gui.ImageExporter.ImageWriterI;
-import jalview.io.HTMLOutput;
-import jalview.jbgui.GAlignmentPanel;
-import jalview.math.AlignmentDimension;
-import jalview.schemes.ResidueProperties;
-import jalview.structure.StructureSelectionManager;
-import jalview.util.Comparison;
-import jalview.util.ImageMaker;
-import jalview.util.MessageManager;
-import jalview.viewmodel.ViewportListenerI;
-import jalview.viewmodel.ViewportRanges;
-
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Container;
@@ -68,6 +44,31 @@ import java.util.List;
 
 import javax.swing.SwingUtilities;
 
+import jalview.analysis.AnnotationSorter;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.bin.Cache;
+import jalview.bin.Console;
+import jalview.bin.Jalview;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.gui.ImageExporter.ImageWriterI;
+import jalview.io.HTMLOutput;
+import jalview.jbgui.GAlignmentPanel;
+import jalview.math.AlignmentDimension;
+import jalview.schemes.ResidueProperties;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.Comparison;
+import jalview.util.ImageMaker;
+import jalview.util.MessageManager;
+import jalview.viewmodel.ViewportListenerI;
+import jalview.viewmodel.ViewportRanges;
+import jalview.workers.VisibleFeaturesAnnotationTracks;
+
 /**
  * DOCUMENT ME!
  * 
@@ -115,6 +116,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
   private CalculationChooser calculationDialog;
 
+  private VisibleFeaturesAnnotationTracks featureCounter;
+
   /**
    * Creates a new AlignmentPanel object.
    * 
@@ -123,13 +126,15 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   public AlignmentPanel(AlignFrame af, final AlignViewport av)
   {
-//     setBackground(Color.white);  // BH 2019
+    // setBackground(Color.white); // BH 2019
     alignFrame = af;
     this.av = av;
     setSeqPanel(new SeqPanel(av, this));
     setIdPanel(new IdPanel(av, this));
 
     setScalePanel(new ScalePanel(av, this));
+    featureCounter = new VisibleFeaturesAnnotationTracks(av,
+            seqPanel.seqCanvas.fr);
 
     idPanelHolder.add(getIdPanel(), BorderLayout.CENTER);
     idwidthAdjuster = new IdwidthAdjuster(this);
@@ -179,6 +184,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     });
 
     final AlignmentPanel ap = this;
+
     propertyChangeListener = new PropertyChangeListener()
     {
       @Override
@@ -472,8 +478,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
         /*
          * Scroll down to make end of search results visible
          */
-        setScrollValues(ranges.getStartRes(), starts + seqIndex - ends
-                + 1);
+        setScrollValues(ranges.getStartRes(), starts + seqIndex - ends + 1);
       }
       /*
        * Else results are already visible - no need to scroll
@@ -573,7 +578,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
     Dimension e = idPanel.getSize();
     alabels.setSize(new Dimension(e.width, annotationHeight));
 
-
     annotationSpaceFillerHolder.setPreferredSize(new Dimension(
             annotationSpaceFillerHolder.getWidth(), annotationHeight));
     annotationScroller.validate();
@@ -826,6 +830,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
   public void paintAlignment(boolean updateOverview,
           boolean updateStructures)
   {
+    featureCounter.updateFeatureAnnotationTracks();
     final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
             av.isShowAutocalculatedAbove());
     sorter.sort(getAlignment().getAlignmentAnnotation(),
@@ -1021,8 +1026,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
      * single graphics context), then reset to (0, scale height)
      */
     alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight);
-    getSeqPanel().seqCanvas.drawPanelForPrinting(alignmentGraphics, startRes,
-            endRes, startSeq, endSeq - 1);
+    getSeqPanel().seqCanvas.drawPanelForPrinting(alignmentGraphics,
+            startRes, endRes, startSeq, endSeq - 1);
     alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
 
     if (av.isShowAnnotation() && (endSeq == alignmentHeight))
@@ -1066,8 +1071,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * 
    * @throws PrinterException
    */
-  public int printWrappedAlignment(int pageWidth, int pageHeight, int pageNumber,
-          Graphics g) throws PrinterException
+  public int printWrappedAlignment(int pageWidth, int pageHeight,
+          int pageNumber, Graphics g) throws PrinterException
   {
     getSeqPanel().seqCanvas.calculateWrappedGeometry(getWidth(),
             getHeight());
@@ -1119,8 +1124,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     g.translate(idWidth, 0);
 
-    getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(g, pageWidth - idWidth,
-            totalHeight, 0);
+    getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(g,
+            pageWidth - idWidth, totalHeight, 0);
 
     if ((pageNumber * pageHeight) < totalHeight)
     {
@@ -1285,13 +1290,13 @@ public class AlignmentPanel extends GAlignmentPanel implements
             String triplet = null;
             if (av.getAlignment().isNucleotide())
             {
-              triplet = ResidueProperties.nucleotideName.get(seq
-                      .getCharAt(column) + "");
+              triplet = ResidueProperties.nucleotideName
+                      .get(seq.getCharAt(column) + "");
             }
             else
             {
-              triplet = ResidueProperties.aa2Triplet.get(seq.getCharAt(column)
-                      + "");
+              triplet = ResidueProperties.aa2Triplet
+                      .get(seq.getCharAt(column) + "");
             }
 
             if (triplet == null)
@@ -1308,7 +1313,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
                 text.append("<area shape=\"rect\" coords=\"")
                         .append((idWidth + column * av.getCharWidth()))
                         .append(",").append(sy).append(",")
-                        .append((idWidth + (column + 1) * av.getCharWidth()))
+                        .append((idWidth
+                                + (column + 1) * av.getCharWidth()))
                         .append(",").append((av.getCharHeight() + sy))
                         .append("\"").append(" onMouseOver=\"toolTip('")
                         .append(seqPos).append(" ").append(triplet);
@@ -1334,7 +1340,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
             }
             if (!Comparison.isGap(seq.getCharAt(column)))
             {
-              List<SequenceFeature> features = seq.findFeatures(column, column);
+              List<SequenceFeature> features = seq.findFeatures(column,
+                      column);
               for (SequenceFeature sf : features)
               {
                 if (sf.isContactFeature())
@@ -1450,6 +1457,11 @@ public class AlignmentPanel extends GAlignmentPanel implements
       annotationPanel = null;
     }
 
+    if (featureCounter != null)
+    {
+      featureCounter.tidyUp();
+      featureCounter = null;
+    }
     if (av != null)
     {
       av.removePropertyChangeListener(propertyChangeListener);
@@ -1547,11 +1559,12 @@ public class AlignmentPanel extends GAlignmentPanel implements
       setAlignFrameView();
     }
   }
+
   public void setAlignFrameView()
   {
     alignFrame.setDisplayedView(this);
   }
-  
+
   @Override
   public StructureSelectionManager getStructureSelectionManager()
   {