X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignViewportI.java;h=2f992a6f499fac16a4edc0d3f55fa943f967085f;hb=6a6fb5010c2cd06b14a1e055eabaeb4848e65d2d;hp=70673286dfb8a0e50e4bf16296785523a6d42dd1;hpb=6dd2a0e7f175aea6f16ded581d7e97f263f7875d;p=jalview.git

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 7067328..2f992a6 100644
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -21,19 +21,23 @@
 package jalview.api;
 
 import jalview.analysis.Conservation;
+import jalview.analysis.TreeModel;
 import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentExportData;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
-import jalview.datamodel.CigarArray;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.ProfilesI;
 import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.renderer.ResidueShaderI;
 import jalview.schemes.ColourSchemeI;
+import jalview.viewmodel.ViewportRanges;
 
 import java.awt.Color;
+import java.awt.Font;
 import java.util.Hashtable;
 import java.util.List;
 import java.util.Map;
@@ -45,7 +49,13 @@ import java.util.Map;
 public interface AlignViewportI extends ViewStyleI
 {
 
-  int getEndRes();
+  /**
+   * Get the ranges object containing details of the start and end sequences and
+   * residues
+   * 
+   * @return
+   */
+  ViewportRanges getRanges();
 
   /**
    * calculate the height for visible annotation, revalidating bounds where
@@ -53,7 +63,7 @@ public interface AlignViewportI extends ViewStyleI
    * 
    * @return total height of annotation
    */
-  public int calcPanelHeight();
+  int calcPanelHeight();
 
   /**
    * Answers true if the viewport has at least one column selected
@@ -77,8 +87,22 @@ public interface AlignViewportI extends ViewStyleI
 
   boolean isNormaliseSequenceLogo();
 
+  boolean isShowInformationHistogram();
+
+  boolean isShowHMMSequenceLogo();
+
+  boolean isNormaliseHMMSequenceLogo();
+
   ColourSchemeI getGlobalColourScheme();
 
+  /**
+   * Returns an object that describes colouring (including any thresholding or
+   * fading) of the alignment
+   * 
+   * @return
+   */
+  ResidueShaderI getResidueShading();
+
   AlignmentI getAlignment();
 
   ColumnSelection getColumnSelection();
@@ -90,12 +114,14 @@ public interface AlignViewportI extends ViewStyleI
    * 
    * @return
    */
-  Hashtable[] getComplementConsensusHash();
+  Hashtable<String, Object>[] getComplementConsensusHash();
 
-  Hashtable[] getRnaStructureConsensusHash();
+  Hashtable<String, Object>[] getRnaStructureConsensusHash();
 
   boolean isIgnoreGapsConsensus();
 
+  boolean isIgnoreBelowBackground();
+
   boolean isCalculationInProgress(AlignmentAnnotation alignmentAnnotation);
 
   AlignmentAnnotation getAlignmentQualityAnnot();
@@ -140,7 +166,7 @@ public interface AlignViewportI extends ViewStyleI
    * 
    * @return
    */
-  AlignCalcManagerI getCalcManager();
+  AlignCalcManagerI2 getCalcManager();
 
   /**
    * get the percentage gaps allowed in a conservation calculation
@@ -160,11 +186,11 @@ public interface AlignViewportI extends ViewStyleI
    * 
    * @param hconsensus
    */
-  void setComplementConsensusHash(Hashtable[] hconsensus);
+  void setComplementConsensusHash(Hashtable<String, Object>[] hconsensus);
 
   /**
    * 
-   * @return the alignment annotatino row for the structure consensus
+   * @return the alignment annotation row for the structure consensus
    *         calculation
    */
   AlignmentAnnotation getAlignmentStrucConsensusAnnotation();
@@ -174,14 +200,17 @@ public interface AlignViewportI extends ViewStyleI
    * 
    * @param hStrucConsensus
    */
-  void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus);
+  void setRnaStructureConsensusHash(
+          Hashtable<String, Object>[] hStrucConsensus);
 
   /**
-   * set global colourscheme
+   * Sets the colour scheme for the background alignment (as distinct from
+   * sub-groups, which may have their own colour schemes). A null value is used
+   * for no residue colour (white).
    * 
-   * @param rhc
+   * @param cs
    */
-  void setGlobalColourScheme(ColourSchemeI rhc);
+  void setGlobalColourScheme(ColourSchemeI cs);
 
   Map<SequenceI, SequenceCollectionI> getHiddenRepSequences();
 
@@ -224,16 +253,6 @@ public interface AlignViewportI extends ViewStyleI
   void clearSequenceColours();
 
   /**
-   * 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.
-   * 
-   * @return String[]
-   */
-  CigarArray getViewAsCigars(boolean selectedRegionOnly);
-
-  /**
    * return a compact representation of the current alignment selection to pass
    * to an analysis function
    * 
@@ -422,9 +441,19 @@ public interface AlignViewportI extends ViewStyleI
    */
   void setFollowHighlight(boolean b);
 
+  /**
+   * configure the feature renderer with predefined feature settings
+   * 
+   * @param featureSettings
+   */
   public void applyFeaturesStyle(FeatureSettingsModelI featureSettings);
 
   /**
+   * Apply the given feature settings on top of existing feature settings.
+   */
+  public void mergeFeaturesStyle(FeatureSettingsModelI featureSettings);
+
+  /**
    * check if current selection group is defined on the view, or is simply a
    * temporary group.
    * 
@@ -452,4 +481,84 @@ public interface AlignViewportI extends ViewStyleI
    * @return search results or null
    */
   SearchResultsI getSearchResults();
+
+  /**
+   * Updates view settings with the given font. You may need to call
+   * AlignmentPanel.fontChanged to update the layout geometry.
+   * 
+   * @param setGrid
+   *          when true, charWidth/height is set according to font metrics
+   */
+  void setFont(Font newFont, boolean b);
+
+  /**
+   * Answers true if split screen protein and cDNA use the same font
+   * 
+   * @return
+   */
+  @Override
+  boolean isProteinFontAsCdna();
+
+  /**
+   * Set the flag for whether split screen protein and cDNA use the same font
+   * 
+   * @return
+   */
+  @Override
+  void setProteinFontAsCdna(boolean b);
+
+  void setHmmProfiles(ProfilesI info);
+
+  ProfilesI getHmmProfiles();
+
+  /**
+   * Registers and starts a worker thread to calculate Information Content
+   * annotation, if it is not already registered
+   * 
+   * @param ap
+   */
+  void initInformationWorker(AlignmentViewPanel ap);
+
+  boolean isInfoLetterHeight();
+
+  public abstract TreeModel getCurrentTree();
+
+  /**
+   * Answers a data bean containing data for export as configured by the
+   * supplied options
+   * 
+   * @param options
+   * @return
+   */
+  AlignmentExportData getAlignExportData(AlignExportSettingsI options);
+
+  public abstract void setCurrentTree(TreeModel tree);
+
+  /**
+   * @param update
+   *          - set the flag for updating structures on next repaint
+   */
+  void setUpdateStructures(boolean update);
+
+  /**
+   *
+   * @return true if structure views will be updated on next refresh
+   */
+  boolean isUpdateStructures();
+
+  /**
+   * check if structure views need to be updated, and clear the flag afterwards.
+   * 
+   * @return if an update is needed
+   */
+  boolean needToUpdateStructureViews();
+
+  /**
+   * Adds sequencegroup to the alignment in the view. Also adds a group to the
+   * complement view if one is defined.
+   * 
+   * @param sequenceGroup
+   *          - a group defined on sequences in the alignment held by the view
+   */
+  void addSequenceGroup(SequenceGroup sequenceGroup);
 }