X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignViewportI.java;h=b09538e0bab0eb409ae5ce41924705b124909541;hb=fbfbbe26bee37143d5279fe4d254a5a89c96b021;hp=f42293d8d6178355ca2bfe3c4e47e2fc552d0281;hpb=ad20cd92225f2ee8c251d39b00b90555d382a616;p=jalview.git

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index f42293d..b09538e 100644
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -1,44 +1,63 @@
 /*
- * 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 ($$Version-Rel$$)
+ * 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.
+ * 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.util.Hashtable;
-import java.util.Map;
-
+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.ColumnSelection;
+import jalview.datamodel.ContactListI;
+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.Iterator;
+import java.util.List;
+import java.util.Map;
 
 /**
  * @author jimp
  * 
  */
-public interface AlignViewportI
+public interface AlignViewportI extends ViewStyleI
 {
 
-  int getCharWidth();
-
-  int getEndRes();
-
-  int getCharHeight();
+  /**
+   * Get the ranges object containing details of the start and end sequences and
+   * residues
+   * 
+   * @return
+   */
+  public ViewportRanges getRanges();
 
   /**
    * calculate the height for visible annotation, revalidating bounds where
@@ -48,6 +67,18 @@ public interface AlignViewportI
    */
   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();
@@ -60,17 +91,30 @@ public interface AlignViewportI
 
   ColourSchemeI getGlobalColourScheme();
 
+  /**
+   * Returns an object that describes colouring (including any thresholding or
+   * fading) of the alignment
+   * 
+   * @return
+   */
+  ResidueShaderI getResidueShading();
+
   AlignmentI getAlignment();
 
   ColumnSelection getColumnSelection();
 
-  Hashtable[] getSequenceConsensusHash();
+  ProfilesI getSequenceConsensusHash();
 
-  Hashtable[] getRnaStructureConsensusHash();
+  /**
+   * Get consensus data table for the cDNA complement of this alignment (if any)
+   * 
+   * @return
+   */
+  Hashtable<String, Object>[] getComplementConsensusHash();
 
-  boolean getIgnoreGapsConsensus();
+  Hashtable<String, Object>[] getRnaStructureConsensusHash();
 
-  boolean getCentreColumnLabels();
+  boolean isIgnoreGapsConsensus();
 
   boolean isCalculationInProgress(AlignmentAnnotation alignmentAnnotation);
 
@@ -86,6 +130,20 @@ public interface AlignViewportI
   AlignmentAnnotation getAlignmentConsensusAnnotation();
 
   /**
+   * get the container for alignment gap annotation
+   * 
+   * @return
+   */
+  AlignmentAnnotation getAlignmentGapAnnotation();
+
+  /**
+   * 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
@@ -93,6 +151,11 @@ public interface AlignViewportI
   boolean isClosed();
 
   /**
+   * Dispose of all references or resources held by the viewport
+   */
+  void dispose();
+
+  /**
    * get the associated calculation thread manager for the view
    * 
    * @return
@@ -110,11 +173,18 @@ public interface AlignViewportI
    * 
    * @param hconsensus
    */
-  void setSequenceConsensusHash(Hashtable[] hconsensus);
+  void setSequenceConsensusHash(ProfilesI hconsensus);
 
   /**
+   * Set the cDNA complement consensus for the viewport
    * 
-   * @return the alignment annotatino row for the structure consensus
+   * @param hconsensus
+   */
+  void setComplementConsensusHash(Hashtable<String, Object>[] hconsensus);
+
+  /**
+   * 
+   * @return the alignment annotation row for the structure consensus
    *         calculation
    */
   AlignmentAnnotation getAlignmentStrucConsensusAnnotation();
@@ -124,14 +194,17 @@ public interface AlignViewportI
    * 
    * @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();
 
@@ -155,4 +228,331 @@ 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();
+
+  /**
+   * 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. 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,
+          boolean isExportHiddenSeqs);
+
+  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);
+
+  /**
+   * 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.
+   * 
+   * @return true if group is defined on the alignment
+   */
+  boolean isSelectionDefinedGroup();
+
+  /**
+   * 
+   * @return true if there are search results on the view
+   */
+  boolean hasSearchResults();
+
+  /**
+   * set the search results for the view
+   * 
+   * @param results
+   *          - or null to clear current results
+   */
+  void setSearchResults(SearchResultsI results);
+
+  /**
+   * get search results for this view (if any)
+   * 
+   * @return search results or null
+   */
+  SearchResultsI getSearchResults();
+
+  ContactListI getContactList(AlignmentAnnotation _aa, int column);
+
+  /**
+   * 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);
+
+  TreeModel getCurrentTree();
+
+  void setCurrentTree(TreeModel tree);
+
+  /**
+   * Answers a data bean containing data for export as configured by the
+   * supplied options
+   * 
+   * @param options
+   * @return
+   */
+  AlignmentExportData getAlignExportData(AlignExportSettingsI options);
+
+  /**
+   * @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);
+
+  /**
+   * Returns an interator over the [start, end] column positions of the visible
+   * regions of the alignment
+   * 
+   * @param selectedRegionOnly
+   *          if true, and the view has a selection region, then only the
+   *          intersection of visible columns with the selection region is
+   *          returned
+   * @return
+   */
+  Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly);
 }