Merge branch 'develop' into bug/JAL-98consensusMemory

[jalview.git] / src / jalview / renderer / AnnotationRenderer.java

diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index 94015de..ed758c5 100644 (file)
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -22,6 +22,7 @@ package jalview.renderer;
 
 import jalview.analysis.AAFrequency;
 import jalview.analysis.CodingUtils;
+import jalview.analysis.Profile;
 import jalview.analysis.Rna;
 import jalview.analysis.StructureFrequency;
 import jalview.api.AlignViewportI;
@@ -30,6 +31,7 @@ import jalview.datamodel.Annotation;
 import jalview.datamodel.ColumnSelection;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ResidueProperties;
+import jalview.util.Platform;
 
 import java.awt.BasicStroke;
 import java.awt.Color;
@@ -57,6 +59,70 @@ public class AnnotationRenderer
    */
   private final boolean debugRedraw;
 
+  private int charWidth, endRes, charHeight;
+
+  private boolean validCharWidth, hasHiddenColumns;
+
+  private FontMetrics fm;
+
+  private final boolean MAC = Platform.isAMac();
+
+  boolean av_renderHistogram = true, av_renderProfile = true,
+          av_normaliseProfile = false;
+
+  ColourSchemeI profcolour = null;
+
+  private ColumnSelection columnSelection;
+
+  private Profile[] hconsensus;
+
+  private Hashtable[] complementConsensus;
+
+  private Hashtable[] hStrucConsensus;
+
+  private boolean av_ignoreGapsConsensus;
+
+  /**
+   * attributes set from AwtRenderPanelI
+   */
+  /**
+   * old image used when data is currently being calculated and cannot be
+   * rendered
+   */
+  private Image fadedImage;
+
+  /**
+   * panel being rendered into
+   */
+  private ImageObserver annotationPanel;
+
+  /**
+   * width of image to render in panel
+   */
+  private int imgWidth;
+
+  /**
+   * offset to beginning of visible area
+   */
+  private int sOffset;
+
+  /**
+   * offset to end of visible area
+   */
+  private int visHeight;
+
+  /**
+   * indicate if the renderer should only render the visible portion of the
+   * annotation given the current view settings
+   */
+  private boolean useClip = true;
+
+  /**
+   * master flag indicating if renderer should ever try to clip. not enabled for
+   * jalview 2.8.1
+   */
+  private boolean canClip = false;
+
   public AnnotationRenderer()
   {
     this(false);
@@ -74,9 +140,21 @@ public class AnnotationRenderer
     this.debugRedraw = debugRedraw;
   }
 
-  void drawStemAnnot(Graphics g, Annotation[] row_annotations,
-          int lastSSX, int x, int y, int iconOffset, int startRes,
-          int column, boolean validRes, boolean validEnd)
+  /**
+   * Remove any references and resources when this object is no longer required
+   */
+  public void dispose()
+  {
+    hconsensus = null;
+    complementConsensus = null;
+    hStrucConsensus = null;
+    fadedImage = null;
+    annotationPanel = null;
+  }
+
+  void drawStemAnnot(Graphics g, Annotation[] row_annotations, int lastSSX,
+          int x, int y, int iconOffset, int startRes, int column,
+          boolean validRes, boolean validEnd)
   {
     g.setColor(STEM_COLOUR);
     int sCol = (lastSSX / charWidth) + startRes;
@@ -134,70 +212,6 @@ public class AnnotationRenderer
     g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7);
   }
 
-  private int charWidth, endRes, charHeight;
-
-  private boolean validCharWidth, hasHiddenColumns;
-
-  private FontMetrics fm;
-
-  private final boolean MAC = jalview.util.Platform.isAMac();
-
-  boolean av_renderHistogram = true, av_renderProfile = true,
-          av_normaliseProfile = false;
-
-  ColourSchemeI profcolour = null;
-
-  private ColumnSelection columnSelection;
-
-  private Hashtable[] hconsensus;
-
-  private Hashtable[] complementConsensus;
-
-  private Hashtable[] hStrucConsensus;
-
-  private boolean av_ignoreGapsConsensus;
-
-  /**
-   * attributes set from AwtRenderPanelI
-   */
-  /**
-   * old image used when data is currently being calculated and cannot be
-   * rendered
-   */
-  private Image fadedImage;
-
-  /**
-   * panel being rendered into
-   */
-  private ImageObserver annotationPanel;
-
-  /**
-   * width of image to render in panel
-   */
-  private int imgWidth;
-
-  /**
-   * offset to beginning of visible area
-   */
-  private int sOffset;
-
-  /**
-   * offset to end of visible area
-   */
-  private int visHeight;
-
-  /**
-   * indicate if the renderer should only render the visible portion of the
-   * annotation given the current view settings
-   */
-  private boolean useClip = true;
-
-  /**
-   * master flag indicating if renderer should ever try to clip. not enabled for
-   * jalview 2.8.1
-   */
-  private boolean canClip = false;
-
   void drawNotCanonicalAnnot(Graphics g, Color nonCanColor,
           Annotation[] row_annotations, int lastSSX, int x, int y,
           int iconOffset, int startRes, int column, boolean validRes,
@@ -220,7 +234,7 @@ public class AnnotationRenderer
             || !dc.equals(row_annotations[column].displayCharacter);
     // System.out.println("Column "+column+" diff up: "+diffupstream+" down:"+diffdownstream);
     // If a closing base pair half of the stem, display a backward arrow
-    if (column > 0 && Rna.isClosingParenthesis(dc.charAt(0)))
+    if (column > 0 && Rna.isClosingParenthesis(dc))
     {
 
       if (diffupstream)
@@ -1072,8 +1086,8 @@ public class AnnotationRenderer
 
   private Color sdNOTCANONICAL_COLOUR;
 
-  void drawGlyphLine(Graphics g, Annotation[] row, int lastSSX,
-          int x, int y, int iconOffset, int startRes, int column,
+  void drawGlyphLine(Graphics g, Annotation[] row, int lastSSX, int x,
+          int y, int iconOffset, int startRes, int column,
           boolean validRes, boolean validEnd)
   {
     g.setColor(GLYPHLINE_COLOR);
@@ -1104,8 +1118,8 @@ public class AnnotationRenderer
 
   }
 
-  void drawHelixAnnot(Graphics g, Annotation[] row, int lastSSX,
-          int x, int y, int iconOffset, int startRes, int column,
+  void drawHelixAnnot(Graphics g, Annotation[] row, int lastSSX, int x,
+          int y, int iconOffset, int startRes, int column,
           boolean validRes, boolean validEnd)
   {
     g.setColor(HELIX_COLOUR);