develop merge

[jalview.git] / src / jalview / workers / AnnotationWorker.java

diff --git a/src/jalview/workers/AnnotationWorker.java b/src/jalview/workers/AnnotationWorker.java
new file mode 100644 (file)
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+++ b/src/jalview/workers/AnnotationWorker.java
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+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.workers;
+
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.gui.AlignFrame;
+import jalview.gui.AlignmentPanel;
+import jalview.gui.FeatureRenderer;
+
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ * A class to create and update one or more alignment annotations, given a
+ * 'calculator'.
+ * 
+ */
+class AnnotationWorker extends AlignCalcWorker
+{
+  /*
+   * the provider of the annotation calculations
+   */
+  AnnotationProviderI counter;
+
+  /**
+   * Constructor
+   * 
+   * @param af
+   * @param counter
+   */
+  public AnnotationWorker(AlignFrame af, AnnotationProviderI counter)
+  {
+    super(af.getViewport(), af.alignPanel);
+    ourAnnots = new ArrayList<AlignmentAnnotation>();
+    this.counter = counter;
+    calcMan.registerWorker(this);
+  }
+
+  @Override
+  public void run()
+  {
+    try
+    {
+      calcMan.notifyStart(this);
+
+      while (!calcMan.notifyWorking(this))
+      {
+        try
+        {
+          Thread.sleep(200);
+        } catch (InterruptedException ex)
+        {
+          ex.printStackTrace();
+        }
+      }
+      if (alignViewport.isClosed())
+      {
+        abortAndDestroy();
+        return;
+      }
+
+      removeAnnotations();
+      AlignmentI alignment = alignViewport.getAlignment();
+      if (alignment != null)
+      {
+        try
+        {
+          List<AlignmentAnnotation> anns = counter.calculateAnnotation(
+                  alignment, new FeatureRenderer((AlignmentPanel) ap));
+          for (AlignmentAnnotation ann : anns)
+          {
+            ann.showAllColLabels = true;
+            ann.graph = AlignmentAnnotation.BAR_GRAPH;
+            ourAnnots.add(ann);
+            alignment.addAnnotation(ann);
+          }
+        } catch (IndexOutOfBoundsException x)
+        {
+          // probable race condition. just finish and return without any fuss.
+          return;
+        }
+      }
+    } catch (OutOfMemoryError error)
+    {
+      ap.raiseOOMWarning("calculating annotations", error);
+      calcMan.workerCannotRun(this);
+    } finally
+    {
+      calcMan.workerComplete(this);
+    }
+
+    if (ap != null)
+    {
+      ap.adjustAnnotationHeight();
+      ap.paintAlignment(true);
+    }
+
+  }
+
+  /**
+   * Remove all our annotations before re-calculating them
+   */
+  void removeAnnotations()
+  {
+    for (AlignmentAnnotation ann : ourAnnots)
+    {
+      alignViewport.getAlignment().deleteAnnotation(ann);
+    }
+    ourAnnots.clear();
+  }
+
+  @Override
+  public void updateAnnotation()
+  {
+    // do nothing
+  }
+}