JAL-1780 more support for export setting for flatfile output

[jalview.git] / src / jalview / api / AlignViewportI.java

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index c49ee39..fa73194 100644 (file)
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -20,6 +20,11 @@
  */
 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;
@@ -31,11 +36,6 @@ 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 java.util.Map;
 public interface AlignViewportI extends ViewStyleI
 {
 
-  int getCharWidth();
-
   int getEndRes();
 
-  int getCharHeight();
-
   /**
    * calculate the height for visible annotation, revalidating bounds where
    * necessary ABSTRACT GUI METHOD
@@ -183,29 +179,6 @@ 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);
 
   Color getSequenceColour(SequenceI seq);
@@ -288,35 +261,8 @@ 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);
@@ -413,4 +359,39 @@ public interface AlignViewportI extends ViewStyleI
    * @return
    */
   String getViewId();
+
+  /**
+   * Return true if view should scroll to show the highlighted region of a
+   * sequence
+   * 
+   * @return
+   */
+  boolean isFollowHighlight();
+
+  /**
+   * Set whether view should scroll to show the highlighted region of a sequence
+   */
+  void setFollowHighlight(boolean b);
+
+  /**
+   * Returns a FeatureRenderer instance
+   * 
+   * @return
+   */
+  public FeatureRenderer getFeatureRenderer();
+
+  /**
+   * Sets a FeatureRenderer for a viewport
+   * 
+   * @param featureRenderer
+   */
+  public void setFeatureRenderer(FeatureRenderer featureRenderer);
+
+  /**
+   * Returns Settings for exporting an Alignment
+   * 
+   * @return
+   */
+  public AlignExportSettingI getExportSettings();
+
 }