X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;fp=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=a48c9103bf0bd478fe58f4b038cb2135b2f3d973;hb=9de04d9b678021165d2f6df691234e7ad7b16f88;hp=daea70d856252eca8048a85612e985caffef71a3;hpb=8d6b113f475c6b5916f7685cfd289e054d95a9ee;p=jalview.git

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index daea70d..a48c910 100644
--- 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;