X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=4a43798975f89f99535fcf4f1523567d638e7a78;hb=3cdecbd752fe2d2d8c7b48ba36343c5188f30c40;hp=de1ffdff15ab53060956320f0c5417e59a8df3e1;hpb=cca50cb3aee94f3ed1a5e504d45b8d8b665f8c5b;p=jalview.git

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index de1ffdf..4a43798 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -165,16 +165,17 @@ public class SeqPanel extends JPanel implements MouseListener,
     int res = 0;
     int x = evt.getX();
 
-    if (av.wrapAlignment)
+    if (av.getWrapAlignment())
     {
 
-      int hgap = av.charHeight;
-      if (av.scaleAboveWrapped)
+      int hgap = av.getCharHeight();
+      if (av.getScaleAboveWrapped())
       {
-        hgap += av.charHeight;
+        hgap += av.getCharHeight();
       }
 
-      int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
+      int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
+              + hgap
               + seqCanvas.getAnnotationHeight();
 
       int y = evt.getY();
@@ -218,15 +219,16 @@ public class SeqPanel extends JPanel implements MouseListener,
     int seq = 0;
     int y = evt.getY();
 
-    if (av.wrapAlignment)
+    if (av.getWrapAlignment())
     {
-      int hgap = av.charHeight;
-      if (av.scaleAboveWrapped)
+      int hgap = av.getCharHeight();
+      if (av.getScaleAboveWrapped())
       {
-        hgap += av.charHeight;
+        hgap += av.getCharHeight();
       }
 
-      int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
+      int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
+              + hgap
               + seqCanvas.getAnnotationHeight();
 
       y -= hgap;
@@ -243,44 +245,6 @@ public class SeqPanel extends JPanel implements MouseListener,
     return seq;
   }
 
-  SequenceFeature[] findFeaturesAtRes(SequenceI sequence, int res)
-  {
-    Vector tmp = new Vector();
-    SequenceFeature[] features = sequence.getSequenceFeatures();
-    if (features != null)
-    {
-      for (int i = 0; i < features.length; i++)
-      {
-        if (av.featuresDisplayed == null
-                || !av.featuresDisplayed.containsKey(features[i].getType()))
-        {
-          continue;
-        }
-
-        if (features[i].featureGroup != null
-                && seqCanvas.fr.featureGroups != null
-                && seqCanvas.fr.featureGroups
-                        .containsKey(features[i].featureGroup)
-                && !((Boolean) seqCanvas.fr.featureGroups
-                        .get(features[i].featureGroup)).booleanValue())
-        {
-          continue;
-        }
-
-        if ((features[i].getBegin() <= res)
-                && (features[i].getEnd() >= res))
-        {
-          tmp.addElement(features[i]);
-        }
-      }
-    }
-
-    features = new SequenceFeature[tmp.size()];
-    tmp.copyInto(features);
-
-    return features;
-  }
-
   void endEditing()
   {
     if (editCommand != null && editCommand.getSize() > 0)
@@ -380,7 +344,7 @@ public class SeqPanel extends JPanel implements MouseListener,
     }
 
     endEditing();
-    if (av.wrapAlignment)
+    if (av.getWrapAlignment())
     {
       ap.scrollToWrappedVisible(seqCanvas.cursorX);
     }
@@ -394,7 +358,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       {
         ap.scrollUp(false);
       }
-      if (!av.wrapAlignment)
+      if (!av.getWrapAlignment())
       {
         while (seqCanvas.cursorX < av.getColumnSelection()
                 .adjustForHiddenColumns(av.startRes))
@@ -743,14 +707,14 @@ public class SeqPanel extends JPanel implements MouseListener,
     }
 
     // use aa to see if the mouse pointer is on a
-    if (av.showSequenceFeatures)
+    if (av.isShowSequenceFeatures())
     {
       int rpos;
-      SequenceFeature[] features = findFeaturesAtRes(
+      List<SequenceFeature> features = ap.getFeatureRenderer().findFeaturesAtRes(
               sequence.getDatasetSequence(),
               rpos = sequence.findPosition(res));
       seqARep.appendFeatures(tooltipText, rpos, features,
-              this.ap.getSeqPanel().seqCanvas.fr.minmax);
+              this.ap.getSeqPanel().seqCanvas.fr.getMinMax());
     }
     if (tooltipText.length() == 6) // <html></html>
     {
@@ -858,7 +822,7 @@ public class SeqPanel extends JPanel implements MouseListener,
   {
     if (mouseWheelPressed)
     {
-      int oldWidth = av.charWidth;
+      int oldWidth = av.getCharWidth();
 
       // Which is bigger, left-right or up-down?
       if (Math.abs(evt.getY() - lastMousePress.getY()) > Math.abs(evt
@@ -881,25 +845,25 @@ public class SeqPanel extends JPanel implements MouseListener,
         }
 
         av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
-        av.charWidth = oldWidth;
+        av.setCharWidth(oldWidth);
         ap.fontChanged();
       }
       else
       {
-        if (evt.getX() < lastMousePress.getX() && av.charWidth > 1)
+        if (evt.getX() < lastMousePress.getX() && av.getCharWidth() > 1)
         {
-          av.charWidth--;
+          av.setCharWidth(av.getCharWidth() - 1);
         }
         else if (evt.getX() > lastMousePress.getX())
         {
-          av.charWidth++;
+          av.setCharWidth(av.getCharWidth() + 1);
         }
 
         ap.paintAlignment(false);
       }
 
       FontMetrics fm = getFontMetrics(av.getFont());
-      av.validCharWidth = fm.charWidth('M') <= av.charWidth;
+      av.validCharWidth = fm.charWidth('M') <= av.getCharWidth();
 
       lastMousePress = evt.getPoint();
 
@@ -1389,21 +1353,21 @@ public class SeqPanel extends JPanel implements MouseListener,
         av.setSelectionGroup(null);
       }
 
-      SequenceFeature[] features = findFeaturesAtRes(
+      List<SequenceFeature> features = seqCanvas.getFeatureRenderer().findFeaturesAtRes(
               sequence.getDatasetSequence(),
               sequence.findPosition(findRes(evt)));
 
-      if (features != null && features.length > 0)
+      if (features != null && features.size()> 0)
       {
         SearchResults highlight = new SearchResults();
-        highlight.addResult(sequence, features[0].getBegin(),
-                features[0].getEnd());
+        highlight.addResult(sequence, features.get(0).getBegin(),
+                features.get(0).getEnd());
         seqCanvas.highlightSearchResults(highlight);
       }
-      if (features != null && features.length > 0)
+      if (features != null && features.size()> 0)
       {
         seqCanvas.getFeatureRenderer().amendFeatures(new SequenceI[]
-        { sequence }, features, false, ap);
+        { sequence }, features.toArray(new SequenceFeature[features.size()]), false, ap);
 
         seqCanvas.highlightSearchResults(null);
       }
@@ -1454,7 +1418,7 @@ public class SeqPanel extends JPanel implements MouseListener,
 
     startWrapBlock = wrappedBlock;
 
-    if (av.wrapAlignment && seq > av.getAlignment().getHeight())
+    if (av.getWrapAlignment() && seq > av.getAlignment().getHeight())
     {
       JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
               .getString("label.cannot_edit_annotations_in_wrapped_view"),
@@ -1518,16 +1482,16 @@ public class SeqPanel extends JPanel implements MouseListener,
 
     if (javax.swing.SwingUtilities.isRightMouseButton(evt))
     {
-      SequenceFeature[] allFeatures = findFeaturesAtRes(
+      List<SequenceFeature> allFeatures = ap.getFeatureRenderer().findFeaturesAtRes(
               sequence.getDatasetSequence(), sequence.findPosition(res));
       Vector links = new Vector();
-      for (int i = 0; i < allFeatures.length; i++)
+      for (SequenceFeature sf:allFeatures)
       {
-        if (allFeatures[i].links != null)
+        if (sf.links != null)
         {
-          for (int j = 0; j < allFeatures[i].links.size(); j++)
+          for (int j = 0; j < sf.links.size(); j++)
           {
-            links.addElement(allFeatures[i].links.elementAt(j));
+            links.addElement(sf.links.elementAt(j));
           }
         }
       }