JAL-969 javadoc and mark interface overrides for clarity

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 760f52d..60ee8d5 100644 (file)
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -20,11 +20,6 @@
  */
 package jalview.api;
 
-import java.awt.Color;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Map;
-
 import jalview.analysis.Conservation;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
@@ -36,6 +31,11 @@ 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
  * 
@@ -195,16 +195,58 @@ public interface AlignViewportI
 
   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);
@@ -245,4 +287,69 @@ public interface AlignViewportI
    * @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);
+
 }

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index daea70d..a48c910 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -1046,32 +1046,24 @@ public abstract class AlignmentViewport implements AlignViewportI
             : hiddenRepSequences.get(seq));
   }
 
+  @Override
   public int adjustForHiddenSeqs(int alignmentIndex)
   {
     return alignment.getHiddenSequences().adjustForHiddenSeqs(
             alignmentIndex);
   }
 
-  // Selection manipulation
-  /**
-   * broadcast selection to any interested parties
-   */
+  @Override
   public abstract void sendSelection();
 
+  @Override
   public void invertColumnSelection()
   {
     colSel.invertColumnSelection(0, alignment.getWidth());
   }
 
-  /**
-   * 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
-   */
+
+  @Override
   public SequenceI[] getSelectionAsNewSequence()
   {
     SequenceI[] sequences;
@@ -1100,12 +1092,7 @@ public abstract class AlignmentViewport implements AlignViewportI
     return sequences;
   }
 
-  /**
-   * get the currently selected sequence objects or all the sequences in the
-   * alignment.
-   * 
-   * @return array of references to sequence objects
-   */
+
   @Override
   public SequenceI[] getSequenceSelection()
   {
@@ -1121,14 +1108,7 @@ public abstract class AlignmentViewport implements AlignViewportI
     return sequences;
   }
 
-  /**
-   * 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[]
-   */
+
   @Override
   public jalview.datamodel.CigarArray getViewAsCigars(
           boolean selectedRegionOnly)
@@ -1138,14 +1118,7 @@ public abstract class AlignmentViewport implements AlignViewportI
             (selectedRegionOnly ? selectionGroup : null));
   }
 
-  /**
-   * 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
-   */
+
   @Override
   public jalview.datamodel.AlignmentView getAlignmentView(
           boolean selectedOnly)
@@ -1153,18 +1126,7 @@ public abstract class AlignmentViewport implements AlignViewportI
     return getAlignmentView(selectedOnly, false);
   }
 
-  /**
-   * 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
-   */
+
   @Override
   public jalview.datamodel.AlignmentView getAlignmentView(
           boolean selectedOnly, boolean markGroups)
@@ -1173,14 +1135,7 @@ public abstract class AlignmentViewport implements AlignViewportI
             hasHiddenColumns, selectedOnly, 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[]
-   */
+
   @Override
   public String[] getViewAsString(boolean selectedRegionOnly)
   {
@@ -1218,15 +1173,8 @@ public abstract class AlignmentViewport implements AlignViewportI
     return selection;
   }
 
-  /**
-   * 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
-   */
+
+  @Override
   public int[][] getVisibleRegionBoundaries(int min, int max)
   {
     Vector regions = new Vector();
@@ -1293,18 +1241,15 @@ public abstract class AlignmentViewport implements AlignViewportI
     return ala;
   }
 
-  /**
-   * @return the padGaps
-   */
+
+  @Override
   public boolean isPadGaps()
   {
     return padGaps;
   }
 
-  /**
-   * @param padGaps
-   *          the padGaps to set
-   */
+
+  @Override
   public void setPadGaps(boolean padGaps)
   {
     this.padGaps = padGaps;
@@ -1316,6 +1261,7 @@ public abstract class AlignmentViewport implements AlignViewportI
    * 
    * @param ap
    */
+  @Override
   public void alignmentChanged(AlignmentViewPanel ap)
   {
     if (isPadGaps())
@@ -1477,6 +1423,7 @@ public abstract class AlignmentViewport implements AlignViewportI
    * 
    * @see jalview.api.AlignViewportI#calcPanelHeight()
    */
+  @Override
   public int calcPanelHeight()
   {
     // setHeight of panels
@@ -1617,11 +1564,13 @@ public abstract class AlignmentViewport implements AlignViewportI
    */
   private boolean colourByReferenceSeq=false;
 
+  @Override
   public boolean isDisplayReferenceSeq()
   {
     return alignment.hasSeqrep() && displayReferenceSeq;
   }
 
+  @Override
   public void setDisplayReferenceSeq(boolean displayReferenceSeq)
   {
     this.displayReferenceSeq = displayReferenceSeq;
@@ -1703,11 +1652,13 @@ public abstract class AlignmentViewport implements AlignViewportI
     return featuresDisplayed;
   }
 
+  @Override
   public void setFeaturesDisplayed(FeaturesDisplayedI featuresDisplayedI)
   {
     featuresDisplayed = featuresDisplayedI;
   }
 
+  @Override
   public boolean areFeaturesDisplayed()
   {
     return featuresDisplayed != null && featuresDisplayed.getRegisterdFeaturesCount()>0;
@@ -1737,11 +1688,13 @@ public abstract class AlignmentViewport implements AlignViewportI
 
   boolean showSeqFeaturesHeight;
 
+  @Override
   public void setShowSequenceFeaturesHeight(boolean selected)
   {
     showSeqFeaturesHeight = selected;
   }
 
+  @Override
   public boolean isShowSequenceFeaturesHeight()
   {
     return showSeqFeaturesHeight;