X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignViewportI.java;h=32f9ecd1a0416162cb2d9d0aebc9ef77fc777da9;hb=0a5ce6145bb76fc7eb8a5cc2670e20453fbedd29;hp=c49ee392d7c336add9e9c1d3be9dc3b473e44ffb;hpb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;p=jalview.git

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index c49ee39..32f9ecd 100644
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -26,6 +26,7 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.CigarArray;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.Profile;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
@@ -43,12 +44,8 @@ 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
@@ -57,6 +54,18 @@ public interface AlignViewportI extends ViewStyleI
    */
   public int calcPanelHeight();
 
+  /**
+   * Answers true if the viewport has at least one column selected
+   * 
+   * @return
+   */
+  boolean hasSelectedColumns();
+
+  /**
+   * Answers true if the viewport has at least one hidden column
+   * 
+   * @return
+   */
   boolean hasHiddenColumns();
 
   boolean isValidCharWidth();
@@ -73,7 +82,7 @@ public interface AlignViewportI extends ViewStyleI
 
   ColumnSelection getColumnSelection();
 
-  Hashtable[] getSequenceConsensusHash();
+  Profile[] getSequenceConsensusHash();
 
   /**
    * Get consensus data table for the cDNA complement of this alignment (if any)
@@ -114,6 +123,11 @@ public interface AlignViewportI extends ViewStyleI
   boolean isClosed();
 
   /**
+   * Dispose of all references or resources held by the viewport
+   */
+  void dispose();
+
+  /**
    * get the associated calculation thread manager for the view
    * 
    * @return
@@ -131,7 +145,7 @@ public interface AlignViewportI extends ViewStyleI
    * 
    * @param hconsensus
    */
-  void setSequenceConsensusHash(Hashtable[] hconsensus);
+  void setSequenceConsensusHash(Profile[] hconsensus);
 
   /**
    * Set the cDNA complement consensus for the viewport
@@ -182,29 +196,6 @@ 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);
 
@@ -262,11 +253,31 @@ public interface AlignViewportI extends ViewStyleI
    * This method returns the visible alignment as text, as seen on the GUI, ie
    * if columns are hidden they will not be returned in the result. Use this for
    * calculating trees, PCA, redundancy etc on views which contain hidden
+   * columns. This method doesn't exclude hidden sequences from the output.
+   *
+   * @param selectedRegionOnly
+   *          - determines if only the selected region or entire alignment is
+   *          exported
+   * @return String[]
+   */
+  String[] getViewAsString(boolean selectedRegionOnly);
+
+  /**
+   * This method returns the visible alignment as text, as seen on the GUI, ie
+   * if columns are hidden they will not be returned in the result. Use this for
+   * calculating trees, PCA, redundancy etc on views which contain hidden
    * columns.
    * 
+   * @param selectedRegionOnly
+   *          - determines if only the selected region or entire alignment is
+   *          exported
+   * @param isExportHiddenSeqs
+   *          - determines if hidden sequences would be exported or not.
+   * 
    * @return String[]
    */
-  String[] getViewAsString(boolean selectedRegionOnly);
+  String[] getViewAsString(boolean selectedRegionOnly,
+          boolean isExportHiddenSeqs);
 
   void setSelectionGroup(SequenceGroup sg);
 
@@ -278,8 +289,11 @@ 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 +302,8 @@ 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 +400,27 @@ 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);
+
+  public void applyFeaturesStyle(FeatureSettingsModelI featureSettings);
+
+  /**
+   * check if current selection group is defined on the view, or is simply a
+   * temporary group.
+   * 
+   * @return true if group is defined on the alignment
+   */
+  boolean isSelectionDefinedGroup();
 }