JAL-969 javadoc and mark interface overrides for clarity

[jalview.git] / src / jalview / viewmodel / AlignmentViewport.java

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 72cd316..a48c910 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -649,9 +649,14 @@ public abstract class AlignmentViewport implements AlignViewportI
     return colSel;
   }
 
+  @Override
   public void setColumnSelection(ColumnSelection colSel)
   {
     this.colSel = colSel;
+    if (colSel != null)
+    {
+      updateHiddenColumns();
+    }
   }
 
   /**
@@ -675,7 +680,7 @@ public abstract class AlignmentViewport implements AlignViewportI
 
   public void updateHiddenColumns()
   {
-    hasHiddenColumns = colSel.getHiddenColumns() != null;
+    hasHiddenColumns = colSel.hasHiddenColumns();
   }
 
   protected boolean hasHiddenRows = false;
@@ -1041,32 +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;
@@ -1095,12 +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()
   {
@@ -1116,14 +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)
@@ -1133,14 +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)
@@ -1148,18 +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)
@@ -1168,14 +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)
   {
@@ -1213,15 +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();
@@ -1288,18 +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;
@@ -1311,6 +1261,7 @@ public abstract class AlignmentViewport implements AlignViewportI
    * 
    * @param ap
    */
+  @Override
   public void alignmentChanged(AlignmentViewPanel ap)
   {
     if (isPadGaps())
@@ -1472,6 +1423,7 @@ public abstract class AlignmentViewport implements AlignViewportI
    * 
    * @see jalview.api.AlignViewportI#calcPanelHeight()
    */
+  @Override
   public int calcPanelHeight()
   {
     // setHeight of panels
@@ -1612,11 +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;
@@ -1698,11 +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;
@@ -1732,11 +1688,13 @@ public abstract class AlignmentViewport implements AlignViewportI
 
   boolean showSeqFeaturesHeight;
 
+  @Override
   public void setShowSequenceFeaturesHeight(boolean selected)
   {
     showSeqFeaturesHeight = selected;
   }
 
+  @Override
   public boolean isShowSequenceFeaturesHeight()
   {
     return showSeqFeaturesHeight;
@@ -1746,37 +1704,26 @@ public abstract class AlignmentViewport implements AlignViewportI
 
   private boolean rightAlignIds = false;
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
-  public boolean getShowAnnotation()
-  {
-    return isShowAnnotation();
-  }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param b
-   *          DOCUMENT ME!
-   */
+  @Override
   public void setShowAnnotation(boolean b)
   {
     showAnnotation = b;
   }
 
+  @Override
   public boolean isShowAnnotation()
   {
     return showAnnotation;
   }
 
+  @Override
   public boolean isRightAlignIds()
   {
     return rightAlignIds;
   }
 
+  @Override
   public void setRightAlignIds(boolean rightAlignIds)
   {
     this.rightAlignIds = rightAlignIds;