X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignViewportI.java;h=5df38d600d8efbb01db37592e92522741035a88d;hb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;hp=1a1cba23d56d9c236a3916520b109ad9e2a19cac;hpb=ed2283c5f54da377a2a2fdbdb7aec75ed7041714;p=jalview.git

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 1a1cba2..5df38d6 100644
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -20,11 +20,6 @@
  */
 package jalview.api;
 
-import java.awt.Color;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Map;
-
 import jalview.analysis.Conservation;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
@@ -36,6 +31,11 @@ import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.schemes.ColourSchemeI;
 
+import java.awt.Color;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+
 /**
  * @author jimp
  * 
@@ -43,12 +43,8 @@ import jalview.schemes.ColourSchemeI;
 public interface AlignViewportI extends ViewStyleI
 {
 
-  int getCharWidth();
-
   int getEndRes();
 
-  int getCharHeight();
-
   /**
    * calculate the height for visible annotation, revalidating bounds where
    * necessary ABSTRACT GUI METHOD
@@ -182,29 +178,6 @@ public interface AlignViewportI extends ViewStyleI
    */
   void updateGroupAnnotationSettings(boolean applyGlobalSettings,
           boolean preserveNewGroupSettings);
-  
-  /**
-   * @return true if a reference sequence is set and should be displayed
-   */
-  public boolean isDisplayReferenceSeq();
-
-  /**
-   * @return set the flag for displaying reference sequences when they are
-   *         available
-   */
-  public void setDisplayReferenceSeq(boolean displayReferenceSeq);
-
-  /**
-   * @return true if colourschemes should render according to reference sequence
-   *         rather than consensus if available
-   */
-  public boolean isColourByReferenceSeq();
-
-  /**
-   * @return true set flag for deciding if colourschemes should render according
-   *         to reference sequence rather than consensus if available
-   */
-  public void setColourByReferenceSeq(boolean colourByReferenceSeq);
 
   void setSequenceColour(SequenceI seq, Color col);
 
@@ -278,8 +251,11 @@ public interface AlignViewportI extends ViewStyleI
 
   /**
    * get a copy of the currently visible alignment annotation
-   * @param selectedOnly if true - trim to selected regions on the alignment
-   * @return an empty list or new alignment annotation objects shown only visible columns trimmed to selected region only
+   * 
+   * @param selectedOnly
+   *          if true - trim to selected regions on the alignment
+   * @return an empty list or new alignment annotation objects shown only
+   *         visible columns trimmed to selected region only
    */
   List<AlignmentAnnotation> getVisibleAlignmentAnnotation(
           boolean selectedOnly);
@@ -288,35 +264,8 @@ public interface AlignViewportI extends ViewStyleI
 
   String getSequenceSetId();
 
-  boolean isShowSequenceFeatures();
-
-  void setShowSequenceFeatures(boolean b);
-
-  /**
-   * 
-   * @param flag
-   *          indicating if annotation panel shown below alignment
-   * 
-   */
-  void setShowAnnotation(boolean b);
-
-  /**
-   * flag indicating if annotation panel shown below alignment
-   * 
-   * @return
-   */
-  boolean isShowAnnotation();
-
-  boolean isRightAlignIds();
-
-  void setRightAlignIds(boolean rightAlignIds);
-
   boolean areFeaturesDisplayed();
 
-  void setShowSequenceFeaturesHeight(boolean selected);
-
-  boolean isShowSequenceFeaturesHeight();
-
   void setFeaturesDisplayed(FeaturesDisplayedI featuresDisplayedI);
 
   void alignmentChanged(AlignmentViewPanel ap);