X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fapi%2FAlignViewportI.java;h=e5336831bb6aaec5fa3ca37e156f1aef7bb22210;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=60ee8d5162cdc2d35b6845d366a6ce007bd548ad;hpb=9de04d9b678021165d2f6df691234e7ad7b16f88;p=jalview.git

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 60ee8d5..e533683 100644
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -40,15 +40,11 @@ import java.util.Map;
  * @author jimp
  * 
  */
-public interface AlignViewportI
+public interface AlignViewportI extends ViewStyleI
 {
 
-  int getCharWidth();
-
   int getEndRes();
 
-  int getCharHeight();
-
   /**
    * calculate the height for visible annotation, revalidating bounds where
    * necessary ABSTRACT GUI METHOD
@@ -75,11 +71,16 @@ public interface AlignViewportI
 
   Hashtable[] getSequenceConsensusHash();
 
-  Hashtable[] getRnaStructureConsensusHash();
+  /**
+   * Get consensus data table for the cDNA complement of this alignment (if any)
+   * 
+   * @return
+   */
+  Hashtable[] getComplementConsensusHash();
 
-  boolean getIgnoreGapsConsensus();
+  Hashtable[] getRnaStructureConsensusHash();
 
-  boolean getCentreColumnLabels();
+  boolean isIgnoreGapsConsensus();
 
   boolean isCalculationInProgress(AlignmentAnnotation alignmentAnnotation);
 
@@ -95,6 +96,13 @@ public interface AlignViewportI
   AlignmentAnnotation getAlignmentConsensusAnnotation();
 
   /**
+   * get the container for cDNA complement consensus annotation
+   * 
+   * @return
+   */
+  AlignmentAnnotation getComplementConsensusAnnotation();
+
+  /**
    * Test to see if viewport is still open and active
    * 
    * @return true indicates that all references to viewport should be dropped
@@ -122,6 +130,13 @@ public interface AlignViewportI
   void setSequenceConsensusHash(Hashtable[] hconsensus);
 
   /**
+   * Set the cDNA complement consensus for the viewport
+   * 
+   * @param hconsensus
+   */
+  void setComplementConsensusHash(Hashtable[] hconsensus);
+
+  /**
    * 
    * @return the alignment annotatino row for the structure consensus
    *         calculation
@@ -163,29 +178,6 @@ public interface AlignViewportI
    */
   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);
 
@@ -259,8 +251,11 @@ public interface AlignViewportI
 
   /**
    * 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);
@@ -269,35 +264,8 @@ public interface AlignViewportI
 
   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);
@@ -320,10 +288,9 @@ public interface AlignViewportI
    *          first column (inclusive, from 0)
    * @param max
    *          last column (exclusive)
-   * @return int[][] range of {start,end} visible positions TODO: change to list
-   *         of int ranges
+   * @return int[][] range of {start,end} visible positions
    */
-  int[][] getVisibleRegionBoundaries(int min, int max);
+  List<int[]> getVisibleRegionBoundaries(int min, int max);
 
   /**
    * This method returns an array of new SequenceI objects derived from the
@@ -352,4 +319,60 @@ public interface AlignViewportI
    */
   int adjustForHiddenSeqs(int alignmentIndex);
 
+  boolean hasHiddenRows();
+
+  /**
+   * 
+   * @return a copy of this view's current display settings
+   */
+  public ViewStyleI getViewStyle();
+
+  /**
+   * update the view's display settings with the given style set
+   * 
+   * @param settingsForView
+   */
+  public void setViewStyle(ViewStyleI settingsForView);
+
+  /**
+   * Returns a viewport which holds the cDna for this (protein), or vice versa,
+   * or null if none is set.
+   * 
+   * @return
+   */
+  AlignViewportI getCodingComplement();
+
+  /**
+   * Sets the viewport which holds the cDna for this (protein), or vice versa.
+   * Implementation should guarantee that the reciprocal relationship is always
+   * set, i.e. each viewport is the complement of the other.
+   */
+  void setCodingComplement(AlignViewportI sl);
+
+  /**
+   * Answers true if viewport hosts DNA/RNA, else false.
+   * 
+   * @return
+   */
+  boolean isNucleotide();
+
+  /**
+   * Returns an id guaranteed to be unique for this viewport.
+   * 
+   * @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);
 }