Refactored alignment viewport to use common base, extended viewport API with getters...

[jalview.git] / src / jalview / gui / ConservationThread.java

diff --git a/src/jalview/gui/ConservationThread.java b/src/jalview/gui/ConservationThread.java
deleted file mode 100644 (file)
index 15ec239..0000000
--- a/src/jalview/gui/ConservationThread.java
+++ /dev/null
@@ -1,103 +0,0 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- * 
- * 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/>.
- */
-package jalview.gui;
-
-import jalview.analysis.Conservation;
-import jalview.datamodel.Annotation;
-
-import java.awt.Color;
-
-class ConservationThread extends Thread
-{
-  /**
-   * 
-   */
-  private AlignViewport alignViewport;
-
-  AlignmentPanel ap;
-
-  public ConservationThread(AlignViewport alignViewport, AlignmentPanel ap)
-  {
-    this.alignViewport = alignViewport;
-    this.ap = ap;
-  }
-
-  public void run()
-  {
-    try
-    {
-      this.alignViewport.updatingConservation = true;
-
-      while (AlignViewport.UPDATING_CONSERVATION)
-      {
-        try
-        {
-          if (ap != null)
-          {
-            ap.paintAlignment(false);
-          }
-          Thread.sleep(200);
-        } catch (Exception ex)
-        {
-          ex.printStackTrace();
-        }
-      }
-
-      AlignViewport.UPDATING_CONSERVATION = true;
-
-      int alWidth;
-      
-      if (alignViewport==null || alignViewport.alignment==null || (alWidth=alignViewport.alignment.getWidth())< 0)
-      {
-        this.alignViewport.updatingConservation = false;
-        AlignViewport.UPDATING_CONSERVATION = false;
-        return;
-      }
-
-      Conservation cons = new jalview.analysis.Conservation("All",
-              jalview.schemes.ResidueProperties.propHash, 3,
-              this.alignViewport.alignment.getSequences(), 0, alWidth - 1);
-
-      cons.calculate();
-      cons.verdict(false, this.alignViewport.ConsPercGaps);
-
-      if (this.alignViewport.quality != null)
-      {
-        cons.findQuality();
-      }
-      cons.completeAnnotations(alignViewport.conservation,
-              alignViewport.quality, 0, alWidth);
-    } catch (OutOfMemoryError error)
-    {
-      new OOMWarning("calculating conservation", error);
-
-      this.alignViewport.conservation = null;
-      this.alignViewport.quality = null;
-
-    }
-
-    AlignViewport.UPDATING_CONSERVATION = false;
-    this.alignViewport.updatingConservation = false;
-
-    if (ap != null)
-    {
-      ap.paintAlignment(true);
-    }
-
-  }
-}