JAL-4390 don't output alignment to text panel and stdout when lots of sequences proce...

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

diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index deb2b6f..ad1fa4a 100644 (file)
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -20,6 +20,18 @@
  */
 package jalview.renderer;
 
+import java.awt.BasicStroke;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.Image;
+import java.awt.geom.AffineTransform;
+import java.awt.image.ImageObserver;
+import java.util.BitSet;
+import java.util.Hashtable;
+
 import jalview.analysis.AAFrequency;
 import jalview.analysis.CodingUtils;
 import jalview.analysis.Rna;
@@ -30,24 +42,14 @@ import jalview.datamodel.Annotation;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.ProfilesI;
+import jalview.renderer.api.AnnotationRendererFactoryI;
+import jalview.renderer.api.AnnotationRowRendererI;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.NucleotideColourScheme;
 import jalview.schemes.ResidueProperties;
 import jalview.schemes.ZappoColourScheme;
 import jalview.util.Platform;
 
-import java.awt.BasicStroke;
-import java.awt.Color;
-import java.awt.Font;
-import java.awt.FontMetrics;
-import java.awt.Graphics;
-import java.awt.Graphics2D;
-import java.awt.Image;
-import java.awt.geom.AffineTransform;
-import java.awt.image.ImageObserver;
-import java.util.BitSet;
-import java.util.Hashtable;
-
 public class AnnotationRenderer
 {
   private static final int UPPER_TO_LOWER = 'a' - 'A'; // 32
@@ -155,6 +157,7 @@ public class AnnotationRenderer
     hStrucConsensus = null;
     fadedImage = null;
     annotationPanel = null;
+    rendererFactoryI = null;
   }
 
   void drawStemAnnot(Graphics g, Annotation[] row_annotations, int lastSSX,
@@ -313,6 +316,7 @@ public class AnnotationRenderer
       useClip = false;
     }
 
+    rendererFactoryI = AnnotationRendererFactory.getRendererFactory();
     updateFromAlignViewport(av);
   }
 
@@ -417,6 +421,10 @@ public class AnnotationRenderer
     return null;
   }
 
+  boolean rna = false;
+
+  private AnnotationRendererFactoryI rendererFactoryI;
+
   /**
    * Render the annotation rows associated with an alignment.
    * 
@@ -460,8 +468,8 @@ public class AnnotationRenderer
     boolean validRes = false;
     boolean validEnd = false;
     boolean labelAllCols = false;
-//    boolean centreColLabels;
-//    boolean centreColLabelsDef = av.isCentreColumnLabels();
+    // boolean centreColLabels;
+    // boolean centreColLabelsDef = av.isCentreColumnLabels();
     boolean scaleColLabel = false;
     final AlignmentAnnotation consensusAnnot = av
             .getAlignmentConsensusAnnotation();
@@ -507,7 +515,7 @@ public class AnnotationRenderer
       {
         continue;
       }
-//      centreColLabels = row.centreColLabels || centreColLabelsDef;
+      // centreColLabels = row.centreColLabels || centreColLabelsDef;
       labelAllCols = row.showAllColLabels;
       scaleColLabel = row.scaleColLabel;
       lastSS = ' ';
@@ -1063,6 +1071,32 @@ public class AnnotationRenderer
                     row.graphMin, row.graphMax, y, renderHistogram,
                     renderProfile, normaliseProfile);
           }
+          else
+          {
+            AnnotationRowRendererI renderer = rendererFactoryI
+                    .getRendererFor(row);
+            if (renderer != null)
+            {
+              renderer.renderRow(g, charWidth, charHeight, hasHiddenColumns,
+                      av, hiddenColumns, columnSelection, row,
+                      row_annotations, startRes, endRes, row.graphMin,
+                      row.graphMax, y);
+            }
+            if (debugRedraw)
+            {
+              if (renderer == null)
+              {
+                System.err
+                        .println("No renderer found for " + row.toString());
+              }
+              else
+              {
+                System.err.println(
+                        "rendered with " + renderer.getClass().toString());
+              }
+            }
+
+          }
         }
       }
       else
@@ -1266,8 +1300,7 @@ public class AnnotationRenderer
         break;
       }
 
-      if (aa_annotations[column] == null
-              || aa_annotations[column - 1] == null)
+      if (aa_annotations[column] == null)
       {
         x++;
         continue;
@@ -1282,6 +1315,25 @@ public class AnnotationRenderer
         g.setColor(aa_annotations[column].colour);
       }
 
+      if (aa_annotations[column - 1] == null
+              && aa_annotations.length > column + 1
+              && aa_annotations[column + 1] == null)
+      {
+        // standalone value
+        y1 = y - (int) (((aa_annotations[column].value - min) / range)
+                * graphHeight);
+        g.drawLine(x * charWidth + charWidth / 4, y1,
+                x * charWidth + 3 * charWidth / 4, y1);
+        x++;
+        continue;
+      }
+
+      if (aa_annotations[column - 1] == null)
+      {
+        x++;
+        continue;
+      }
+
       y1 = y - (int) (((aa_annotations[column - 1].value - min) / range)
               * graphHeight);
       y2 = y - (int) (((aa_annotations[column].value - min) / range)