X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignViewportI.java;h=ace7ddb19535f6314e8e1296cfcaf6ac2d7c5453;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=15e5f1d868b7c3074ca7fe09e5e99673ec35ce97;hpb=e3ff86bf4b17ec3cf58bfe8fdb152bfc431765b3;p=jalview.git

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 15e5f1d..ace7ddb 100644
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -1,26 +1,26 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 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.
+ * 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/>.
+ * 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.awt.Color;
-import java.util.Hashtable;
-import java.util.Map;
-
+import jalview.analysis.Conservation;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
@@ -31,19 +31,20 @@ 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
  * 
  */
-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
@@ -70,11 +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);
 
@@ -90,6 +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
@@ -117,6 +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
@@ -159,23 +179,200 @@ public interface AlignViewportI
   void updateGroupAnnotationSettings(boolean applyGlobalSettings,
           boolean preserveNewGroupSettings);
 
+  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 areFeaturesDisplayed();
+
+  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
+   */
+  List<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();
+
+  /**
+   * 
+   * @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);
 }