JAL-2009 added programmatic custom feature setting to show insertion position for...

[jalview.git] / src / jalview / appletgui / AlignViewport.java

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index b0e29da..09e6562 100644 (file)
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -20,14 +20,14 @@
  */
 package jalview.appletgui;
 
-import java.awt.Font;
-
 import jalview.analysis.NJTree;
 import jalview.api.AlignViewportI;
+import jalview.api.FeatureSettingsModelI;
 import jalview.bin.JalviewLite;
 import jalview.commands.CommandI;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SearchResults;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
@@ -39,17 +39,11 @@ import jalview.structure.StructureSelectionManager;
 import jalview.structure.VamsasSource;
 import jalview.viewmodel.AlignmentViewport;
 
+import java.awt.Font;
+
 public class AlignViewport extends AlignmentViewport implements
-        AlignViewportI, SelectionSource, VamsasSource, CommandListener
+        SelectionSource, VamsasSource, CommandListener
 {
-  int startRes;
-
-  int endRes;
-
-  int startSeq;
-
-  int endSeq;
-
   boolean cursorMode = false;
 
   Font font = new Font("SansSerif", Font.PLAIN, 10);
@@ -64,6 +58,7 @@ public class AlignViewport extends AlignmentViewport implements
 
   private AnnotationColumnChooser annotationColumnSelectionState;
 
+  @Override
   public void finalize()
   {
     applet = null;
@@ -103,7 +98,7 @@ public class AlignViewport extends AlignmentViewport implements
                           + widthScale + "). Ignoring.");
           widthScale = 1;
         }
-        if (applet.debug)
+        if (JalviewLite.debug)
         {
           System.err
                   .println("Alignment character width scaling factor is now "
@@ -126,7 +121,7 @@ public class AlignViewport extends AlignmentViewport implements
                           + heightScale + "). Ignoring.");
           heightScale = 1;
         }
-        if (applet.debug)
+        if (JalviewLite.debug)
         {
           System.err
                   .println("Alignment character height scaling factor is now "
@@ -170,9 +165,9 @@ public class AlignViewport extends AlignmentViewport implements
       }
       sortByTree = applet.getDefaultParameter("sortByTree", sortByTree);
 
-      followHighlight = applet.getDefaultParameter("automaticScrolling",
-              followHighlight);
-      followSelection = followHighlight;
+      setFollowHighlight(applet.getDefaultParameter("automaticScrolling",
+              isFollowHighlight()));
+      followSelection = isFollowHighlight();
 
       showSequenceLogo = applet.getDefaultParameter("showSequenceLogo",
               showSequenceLogo);
@@ -194,8 +189,13 @@ public class AlignViewport extends AlignmentViewport implements
 
     if (applet != null)
     {
-      String colour = applet.getParameter("defaultColour");
-
+      String colour = al.isNucleotide() ? applet
+              .getParameter("defaultColourNuc") : applet
+              .getParameter("defaultColourProt");
+      if (colour == null)
+      {
+        colour = applet.getParameter("defaultColour");
+      }
       if (colour == null)
       {
         colour = applet.getParameter("userDefinedColour");
@@ -262,64 +262,6 @@ public class AlignViewport extends AlignmentViewport implements
     return sq;
   }
 
-  public int getStartRes()
-  {
-    return startRes;
-  }
-
-  public int getEndRes()
-  {
-    return endRes;
-  }
-
-  public int getStartSeq()
-  {
-    return startSeq;
-  }
-
-  public void setStartRes(int res)
-  {
-    this.startRes = res;
-  }
-
-  public void setStartSeq(int seq)
-  {
-    this.startSeq = seq;
-  }
-
-  public void setEndRes(int res)
-  {
-    if (res > alignment.getWidth() - 1)
-    {
-      // log.System.out.println(" Corrected res from " + res + " to maximum " +
-      // (alignment.getWidth()-1));
-      res = alignment.getWidth() - 1;
-    }
-    if (res < 0)
-    {
-      res = 0;
-    }
-    this.endRes = res;
-  }
-
-  public void setEndSeq(int seq)
-  {
-    if (seq > alignment.getHeight())
-    {
-      seq = alignment.getHeight();
-    }
-    if (seq < 0)
-    {
-      seq = 0;
-    }
-    this.endSeq = seq;
-  }
-
-  public int getEndSeq()
-  {
-    return endSeq;
-  }
-
   java.awt.Frame nullFrame;
 
   protected FeatureSettings featureSettings = null;
@@ -352,7 +294,6 @@ public class AlignViewport extends AlignmentViewport implements
     return font;
   }
 
-
   public void resetSeqLimits(int height)
   {
     setEndSeq(height / getCharHeight());
@@ -368,7 +309,6 @@ public class AlignViewport extends AlignmentViewport implements
     return currentTree;
   }
 
-
   boolean centreColumnLabels;
 
   public boolean getCentreColumnLabels()
@@ -376,13 +316,6 @@ public class AlignViewport extends AlignmentViewport implements
     return centreColumnLabels;
   }
 
-  public boolean followHighlight = true;
-
-  public boolean getFollowHighlight()
-  {
-    return followHighlight;
-  }
-
   public boolean followSelection = true;
 
   /**
@@ -394,11 +327,12 @@ public class AlignViewport extends AlignmentViewport implements
     return followSelection;
   }
 
+  @Override
   public void sendSelection()
   {
     getStructureSelectionManager().sendSelection(
-                    new SequenceGroup(getSelectionGroup()),
-                    new ColumnSelection(getColumnSelection()), this);
+            new SequenceGroup(getSelectionGroup()),
+            new ColumnSelection(getColumnSelection()), this);
   }
 
   /**
@@ -447,6 +381,7 @@ public class AlignViewport extends AlignmentViewport implements
     }
   }
 
+  @Override
   public boolean isNormaliseSequenceLogo()
   {
     return normaliseSequenceLogo;
@@ -461,6 +396,7 @@ public class AlignViewport extends AlignmentViewport implements
    * 
    * @return true if alignment characters should be displayed
    */
+  @Override
   public boolean isValidCharWidth()
   {
     return validCharWidth;
@@ -514,4 +450,43 @@ public class AlignViewport extends AlignmentViewport implements
     return this;
   }
 
+  /**
+   * If this viewport has a (Protein/cDNA) complement, then scroll the
+   * complementary alignment to match this one.
+   */
+  public void scrollComplementaryAlignment(AlignmentPanel complementPanel)
+  {
+    if (complementPanel == null)
+    {
+      return;
+    }
+
+    /*
+     * Populate a SearchResults object with the mapped location to scroll to. If
+     * there is no complement, or it is not following highlights, or no mapping
+     * is found, the result will be empty.
+     */
+    SearchResults sr = new SearchResults();
+    int seqOffset = findComplementScrollTarget(sr);
+    if (!sr.isEmpty())
+    {
+      complementPanel.setFollowingComplementScroll(true);
+      complementPanel.scrollToCentre(sr, seqOffset);
+    }
+  }
+
+  /**
+   * Applies the supplied feature settings descriptor to currently known
+   * features. This supports an 'initial configuration' of feature colouring
+   * based on a preset or user favourite. This may then be modified in the usual
+   * way using the Feature Settings dialogue.
+   * 
+   * @param featureSettings
+   */
+  @Override
+  public void applyFeaturesStyle(FeatureSettingsModelI featureSettings)
+  {
+    // TODO implement for applet
+  }
+
 }