X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignViewportI.java;h=6faa13368dbaeb0f788d5f5758d456148364f52e;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=6688e2704ab71bb970ae90f825a08f8c01cb0776;hpb=56304e6a5df26368b08a42423919ed315ba3fffb;p=jalview.git

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 6688e27..6faa133 100644
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -1,19 +1,44 @@
-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
  * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.api;
 
-import java.util.Hashtable;
-
+import jalview.analysis.Conservation;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.CigarArray;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
 import jalview.schemes.ColourSchemeI;
-import jalview.schemes.RNAHelicesColour;
+
+import java.awt.Color;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
 
 /**
  * @author jimp
- *
+ * 
  */
 public interface AlignViewportI
 {
@@ -24,6 +49,14 @@ public interface AlignViewportI
 
   int getCharHeight();
 
+  /**
+   * calculate the height for visible annotation, revalidating bounds where
+   * necessary ABSTRACT GUI METHOD
+   * 
+   * @return total height of annotation
+   */
+  public int calcPanelHeight();
+
   boolean hasHiddenColumns();
 
   boolean isValidCharWidth();
@@ -53,23 +86,28 @@ public interface AlignViewportI
   AlignmentAnnotation getAlignmentQualityAnnot();
 
   AlignmentAnnotation getAlignmentConservationAnnotation();
+
   /**
    * get the container for alignment consensus annotation
+   * 
    * @return
    */
   AlignmentAnnotation getAlignmentConsensusAnnotation();
 
   /**
    * Test to see if viewport is still open and active
-   * @return true indicates that all references to viewport should be dropped 
+   * 
+   * @return true indicates that all references to viewport should be dropped
    */
   boolean isClosed();
+
   /**
    * get the associated calculation thread manager for the view
+   * 
    * @return
    */
   AlignCalcManagerI getCalcManager();
-  
+
   /**
    * get the percentage gaps allowed in a conservation calculation
    * 
@@ -78,26 +116,242 @@ public interface AlignViewportI
 
   /**
    * set the consensus result object for the viewport
+   * 
    * @param hconsensus
    */
   void setSequenceConsensusHash(Hashtable[] hconsensus);
 
   /**
    * 
-   * @return the alignment annotatino row for the structure consensus calculation
+   * @return the alignment annotatino row for the structure consensus
+   *         calculation
    */
   AlignmentAnnotation getAlignmentStrucConsensusAnnotation();
 
   /**
    * set the Rna structure consensus result object for the viewport
-   * @param hStrucConsensus 
+   * 
+   * @param hStrucConsensus
    */
   void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus);
 
   /**
    * set global colourscheme
+   * 
    * @param rhc
    */
   void setGlobalColourScheme(ColourSchemeI rhc);
 
+  Map<SequenceI, SequenceCollectionI> getHiddenRepSequences();
+
+  void setHiddenRepSequences(
+          Map<SequenceI, SequenceCollectionI> hiddenRepSequences);
+
+  /**
+   * hides or shows dynamic annotation rows based on groups and group and
+   * alignment associated auto-annotation state flags apply the current
+   * group/autoannotation settings to the alignment view. Usually you should
+   * call the AlignmentViewPanel.adjustAnnotationHeight() method afterwards to
+   * ensure the annotation panel bounds are set correctly.
+   * 
+   * @param applyGlobalSettings
+   *          - apply to all autoannotation rows or just the ones associated
+   *          with the current visible region
+   * @param preserveNewGroupSettings
+   *          - don't apply global settings to groups which don't already have
+   *          group associated annotation
+   */
+  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);
+
+  void updateSequenceIdColours();
+
+  SequenceGroup getSelectionGroup();
+
+  /**
+   * get the currently selected sequence objects or all the sequences in the
+   * alignment. TODO: change to List<>
+   * 
+   * @return array of references to sequence objects
+   */
+  SequenceI[] getSequenceSelection();
+
+  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
+   * 
+   * @param selectedOnly
+   *          boolean true to just return the selected view
+   * @return AlignmentView
+   */
+  AlignmentView getAlignmentView(boolean selectedOnly);
+
+  /**
+   * return a compact representation of the current alignment selection to pass
+   * to an analysis function
+   * 
+   * @param selectedOnly
+   *          boolean true to just return the selected view
+   * @param markGroups
+   *          boolean true to annotate the alignment view with groups on the
+   *          alignment (and intersecting with selected region if selectedOnly
+   *          is true)
+   * @return AlignmentView
+   */
+  AlignmentView getAlignmentView(boolean selectedOnly, boolean markGroups);
+
+  /**
+   * 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[]
+   */
+  String[] getViewAsString(boolean selectedRegionOnly);
+
+  void setSelectionGroup(SequenceGroup sg);
+
+  char getGapCharacter();
+
+  void setColumnSelection(ColumnSelection cs);
+
+  void setConservation(Conservation cons);
+
+  /**
+   * 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
+   */
+  List<AlignmentAnnotation> getVisibleAlignmentAnnotation(
+          boolean selectedOnly);
+
+  FeaturesDisplayedI getFeaturesDisplayed();
+
+  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);
+
+  /**
+   * @return the padGaps
+   */
+  boolean isPadGaps();
+
+  /**
+   * @param padGaps
+   *          the padGaps to set
+   */
+  void setPadGaps(boolean padGaps);
+
+  /**
+   * return visible region boundaries within given column range
+   * 
+   * @param min
+   *          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
+   */
+  int[][] getVisibleRegionBoundaries(int min, int max);
+
+  /**
+   * This method returns an array of new SequenceI objects derived from the
+   * whole alignment or just the current selection with start and end points
+   * adjusted
+   * 
+   * @note if you need references to the actual SequenceI objects in the
+   *       alignment or currently selected then use getSequenceSelection()
+   * @return selection as new sequenceI objects
+   */
+  SequenceI[] getSelectionAsNewSequence();
+
+  void invertColumnSelection();
+
+  /**
+   * broadcast selection to any interested parties
+   */
+  void sendSelection();
+
+  /**
+   * calculate the row position for alignmentIndex if all hidden sequences were
+   * shown
+   * 
+   * @param alignmentIndex
+   * @return adjusted row position
+   */
+  int adjustForHiddenSeqs(int alignmentIndex);
+
+  boolean hasHiddenRows();
+
 }