JAL-1989 more unit tests and encapsulation for ColumnSelection

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

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 3f1946e..c4ae76d 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -95,6 +95,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param name
    * @see jalview.api.ViewStyleI#setFontName(java.lang.String)
    */
+  @Override
   public void setFontName(String name)
   {
     viewStyle.setFontName(name);
@@ -104,6 +105,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param style
    * @see jalview.api.ViewStyleI#setFontStyle(int)
    */
+  @Override
   public void setFontStyle(int style)
   {
     viewStyle.setFontStyle(style);
@@ -113,6 +115,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param size
    * @see jalview.api.ViewStyleI#setFontSize(int)
    */
+  @Override
   public void setFontSize(int size)
   {
     viewStyle.setFontSize(size);
@@ -122,6 +125,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getFontStyle()
    */
+  @Override
   public int getFontStyle()
   {
     return viewStyle.getFontStyle();
@@ -131,6 +135,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getFontName()
    */
+  @Override
   public String getFontName()
   {
     return viewStyle.getFontName();
@@ -140,6 +145,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getFontSize()
    */
+  @Override
   public int getFontSize()
   {
     return viewStyle.getFontSize();
@@ -149,6 +155,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param upperCasebold
    * @see jalview.api.ViewStyleI#setUpperCasebold(boolean)
    */
+  @Override
   public void setUpperCasebold(boolean upperCasebold)
   {
     viewStyle.setUpperCasebold(upperCasebold);
@@ -158,6 +165,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#isUpperCasebold()
    */
+  @Override
   public boolean isUpperCasebold()
   {
     return viewStyle.isUpperCasebold();
@@ -167,6 +175,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#isSeqNameItalics()
    */
+  @Override
   public boolean isSeqNameItalics()
   {
     return viewStyle.isSeqNameItalics();
@@ -176,6 +185,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param colourByReferenceSeq
    * @see jalview.api.ViewStyleI#setColourByReferenceSeq(boolean)
    */
+  @Override
   public void setColourByReferenceSeq(boolean colourByReferenceSeq)
   {
     viewStyle.setColourByReferenceSeq(colourByReferenceSeq);
@@ -185,6 +195,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param b
    * @see jalview.api.ViewStyleI#setColourAppliesToAllGroups(boolean)
    */
+  @Override
   public void setColourAppliesToAllGroups(boolean b)
   {
     viewStyle.setColourAppliesToAllGroups(b);
@@ -194,6 +205,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getColourAppliesToAllGroups()
    */
+  @Override
   public boolean getColourAppliesToAllGroups()
   {
     return viewStyle.getColourAppliesToAllGroups();
@@ -203,6 +215,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getAbovePIDThreshold()
    */
+  @Override
   public boolean getAbovePIDThreshold()
   {
     return viewStyle.getAbovePIDThreshold();
@@ -212,6 +225,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param inc
    * @see jalview.api.ViewStyleI#setIncrement(int)
    */
+  @Override
   public void setIncrement(int inc)
   {
     viewStyle.setIncrement(inc);
@@ -221,6 +235,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getIncrement()
    */
+  @Override
   public int getIncrement()
   {
     return viewStyle.getIncrement();
@@ -230,6 +245,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param b
    * @see jalview.api.ViewStyleI#setConservationSelected(boolean)
    */
+  @Override
   public void setConservationSelected(boolean b)
   {
     viewStyle.setConservationSelected(b);
@@ -239,6 +255,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param show
    * @see jalview.api.ViewStyleI#setShowHiddenMarkers(boolean)
    */
+  @Override
   public void setShowHiddenMarkers(boolean show)
   {
     viewStyle.setShowHiddenMarkers(show);
@@ -248,6 +265,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getShowHiddenMarkers()
    */
+  @Override
   public boolean getShowHiddenMarkers()
   {
     return viewStyle.getShowHiddenMarkers();
@@ -257,6 +275,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param b
    * @see jalview.api.ViewStyleI#setScaleRightWrapped(boolean)
    */
+  @Override
   public void setScaleRightWrapped(boolean b)
   {
     viewStyle.setScaleRightWrapped(b);
@@ -266,6 +285,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param b
    * @see jalview.api.ViewStyleI#setScaleLeftWrapped(boolean)
    */
+  @Override
   public void setScaleLeftWrapped(boolean b)
   {
     viewStyle.setScaleLeftWrapped(b);
@@ -275,6 +295,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param b
    * @see jalview.api.ViewStyleI#setScaleAboveWrapped(boolean)
    */
+  @Override
   public void setScaleAboveWrapped(boolean b)
   {
     viewStyle.setScaleAboveWrapped(b);
@@ -284,6 +305,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getScaleLeftWrapped()
    */
+  @Override
   public boolean getScaleLeftWrapped()
   {
     return viewStyle.getScaleLeftWrapped();
@@ -293,6 +315,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getScaleAboveWrapped()
    */
+  @Override
   public boolean getScaleAboveWrapped()
   {
     return viewStyle.getScaleAboveWrapped();
@@ -302,6 +325,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getScaleRightWrapped()
    */
+  @Override
   public boolean getScaleRightWrapped()
   {
     return viewStyle.getScaleRightWrapped();
@@ -311,6 +335,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param b
    * @see jalview.api.ViewStyleI#setAbovePIDThreshold(boolean)
    */
+  @Override
   public void setAbovePIDThreshold(boolean b)
   {
     viewStyle.setAbovePIDThreshold(b);
@@ -320,6 +345,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param thresh
    * @see jalview.api.ViewStyleI#setThreshold(int)
    */
+  @Override
   public void setThreshold(int thresh)
   {
     viewStyle.setThreshold(thresh);
@@ -329,6 +355,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getThreshold()
    */
+  @Override
   public int getThreshold()
   {
     return viewStyle.getThreshold();
@@ -338,6 +365,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getShowJVSuffix()
    */
+  @Override
   public boolean getShowJVSuffix()
   {
     return viewStyle.getShowJVSuffix();
@@ -347,6 +375,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param b
    * @see jalview.api.ViewStyleI#setShowJVSuffix(boolean)
    */
+  @Override
   public void setShowJVSuffix(boolean b)
   {
     viewStyle.setShowJVSuffix(b);
@@ -356,6 +385,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param state
    * @see jalview.api.ViewStyleI#setWrapAlignment(boolean)
    */
+  @Override
   public void setWrapAlignment(boolean state)
   {
     viewStyle.setWrapAlignment(state);
@@ -365,6 +395,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param state
    * @see jalview.api.ViewStyleI#setShowText(boolean)
    */
+  @Override
   public void setShowText(boolean state)
   {
     viewStyle.setShowText(state);
@@ -374,6 +405,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param state
    * @see jalview.api.ViewStyleI#setRenderGaps(boolean)
    */
+  @Override
   public void setRenderGaps(boolean state)
   {
     viewStyle.setRenderGaps(state);
@@ -383,6 +415,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getColourText()
    */
+  @Override
   public boolean getColourText()
   {
     return viewStyle.getColourText();
@@ -392,6 +425,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param state
    * @see jalview.api.ViewStyleI#setColourText(boolean)
    */
+  @Override
   public void setColourText(boolean state)
   {
     viewStyle.setColourText(state);
@@ -401,6 +435,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getWrapAlignment()
    */
+  @Override
   public boolean getWrapAlignment()
   {
     return viewStyle.getWrapAlignment();
@@ -410,6 +445,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getShowText()
    */
+  @Override
   public boolean getShowText()
   {
     return viewStyle.getShowText();
@@ -419,6 +455,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getWrappedWidth()
    */
+  @Override
   public int getWrappedWidth()
   {
     return viewStyle.getWrappedWidth();
@@ -428,6 +465,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param w
    * @see jalview.api.ViewStyleI#setWrappedWidth(int)
    */
+  @Override
   public void setWrappedWidth(int w)
   {
     viewStyle.setWrappedWidth(w);
@@ -437,6 +475,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getCharHeight()
    */
+  @Override
   public int getCharHeight()
   {
     return viewStyle.getCharHeight();
@@ -446,6 +485,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param h
    * @see jalview.api.ViewStyleI#setCharHeight(int)
    */
+  @Override
   public void setCharHeight(int h)
   {
     viewStyle.setCharHeight(h);
@@ -455,6 +495,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getCharWidth()
    */
+  @Override
   public int getCharWidth()
   {
     return viewStyle.getCharWidth();
@@ -464,6 +505,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param w
    * @see jalview.api.ViewStyleI#setCharWidth(int)
    */
+  @Override
   public void setCharWidth(int w)
   {
     viewStyle.setCharWidth(w);
@@ -473,6 +515,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getShowBoxes()
    */
+  @Override
   public boolean getShowBoxes()
   {
     return viewStyle.getShowBoxes();
@@ -482,6 +525,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getShowUnconserved()
    */
+  @Override
   public boolean getShowUnconserved()
   {
     return viewStyle.getShowUnconserved();
@@ -491,6 +535,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param showunconserved
    * @see jalview.api.ViewStyleI#setShowUnconserved(boolean)
    */
+  @Override
   public void setShowUnconserved(boolean showunconserved)
   {
     viewStyle.setShowUnconserved(showunconserved);
@@ -500,6 +545,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param default1
    * @see jalview.api.ViewStyleI#setSeqNameItalics(boolean)
    */
+  @Override
   public void setSeqNameItalics(boolean default1)
   {
     viewStyle.setSeqNameItalics(default1);
@@ -1147,7 +1193,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    */
   public boolean isColSelChanged(boolean b)
   {
-    int hc = (colSel == null || colSel.size() == 0) ? -1 : colSel
+    int hc = (colSel == null || colSel.isEmpty()) ? -1 : colSel
             .hashCode();
     if (hc != -1 && hc != colselhash)
     {
@@ -1242,7 +1288,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   public void hideSelectedColumns()
   {
-    if (colSel.size() < 1)
+    if (colSel.isEmpty())
     {
       return;
     }
@@ -2115,6 +2161,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getTextColour()
    */
+  @Override
   public Color getTextColour()
   {
     return viewStyle.getTextColour();
@@ -2124,6 +2171,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getTextColour2()
    */
+  @Override
   public Color getTextColour2()
   {
     return viewStyle.getTextColour2();
@@ -2133,6 +2181,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getThresholdTextColour()
    */
+  @Override
   public int getThresholdTextColour()
   {
     return viewStyle.getThresholdTextColour();
@@ -2142,6 +2191,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#isConservationColourSelected()
    */
+  @Override
   public boolean isConservationColourSelected()
   {
     return viewStyle.isConservationColourSelected();
@@ -2151,6 +2201,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#isRenderGaps()
    */
+  @Override
   public boolean isRenderGaps()
   {
     return viewStyle.isRenderGaps();
@@ -2160,6 +2211,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#isShowColourText()
    */
+  @Override
   public boolean isShowColourText()
   {
     return viewStyle.isShowColourText();
@@ -2169,6 +2221,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param conservationColourSelected
    * @see jalview.api.ViewStyleI#setConservationColourSelected(boolean)
    */
+  @Override
   public void setConservationColourSelected(
           boolean conservationColourSelected)
   {
@@ -2179,6 +2232,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param showColourText
    * @see jalview.api.ViewStyleI#setShowColourText(boolean)
    */
+  @Override
   public void setShowColourText(boolean showColourText)
   {
     viewStyle.setShowColourText(showColourText);
@@ -2188,6 +2242,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param textColour
    * @see jalview.api.ViewStyleI#setTextColour(java.awt.Color)
    */
+  @Override
   public void setTextColour(Color textColour)
   {
     viewStyle.setTextColour(textColour);
@@ -2197,6 +2252,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param thresholdTextColour
    * @see jalview.api.ViewStyleI#setThresholdTextColour(int)
    */
+  @Override
   public void setThresholdTextColour(int thresholdTextColour)
   {
     viewStyle.setThresholdTextColour(thresholdTextColour);
@@ -2206,6 +2262,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param textColour2
    * @see jalview.api.ViewStyleI#setTextColour2(java.awt.Color)
    */
+  @Override
   public void setTextColour2(Color textColour2)
   {
     viewStyle.setTextColour2(textColour2);
@@ -2233,6 +2290,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getIdWidth()
    */
+  @Override
   public int getIdWidth()
   {
     return viewStyle.getIdWidth();
@@ -2242,6 +2300,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param i
    * @see jalview.api.ViewStyleI#setIdWidth(int)
    */
+  @Override
   public void setIdWidth(int i)
   {
     viewStyle.setIdWidth(i);
@@ -2251,6 +2310,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#isCentreColumnLabels()
    */
+  @Override
   public boolean isCentreColumnLabels()
   {
     return viewStyle.isCentreColumnLabels();
@@ -2260,6 +2320,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param centreColumnLabels
    * @see jalview.api.ViewStyleI#setCentreColumnLabels(boolean)
    */
+  @Override
   public void setCentreColumnLabels(boolean centreColumnLabels)
   {
     viewStyle.setCentreColumnLabels(centreColumnLabels);
@@ -2269,6 +2330,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param showdbrefs
    * @see jalview.api.ViewStyleI#setShowDBRefs(boolean)
    */
+  @Override
   public void setShowDBRefs(boolean showdbrefs)
   {
     viewStyle.setShowDBRefs(showdbrefs);
@@ -2278,6 +2340,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#isShowDBRefs()
    */
+  @Override
   public boolean isShowDBRefs()
   {
     return viewStyle.isShowDBRefs();
@@ -2287,6 +2350,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#isShowNPFeats()
    */
+  @Override
   public boolean isShowNPFeats()
   {
     return viewStyle.isShowNPFeats();
@@ -2296,6 +2360,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param shownpfeats
    * @see jalview.api.ViewStyleI#setShowNPFeats(boolean)
    */
+  @Override
   public void setShowNPFeats(boolean shownpfeats)
   {
     viewStyle.setShowNPFeats(shownpfeats);
@@ -2428,6 +2493,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
     return startRes;
   }
 
+  @Override
   public int getEndRes()
   {
     return endRes;