JAL-1432 updated copyright notices

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 8978fd7..c05406e 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -1,19 +1,20 @@
 /*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 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.
  */
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
@@ -69,7 +70,8 @@ import java.util.Vector;
  * @author $author$
  * @version $Revision: 1.141 $
  */
-public class AlignViewport extends AlignmentViewport implements SelectionSource, VamsasSource, AlignViewportI
+public class AlignViewport extends AlignmentViewport implements
+        SelectionSource, VamsasSource, AlignViewportI
 {
   int startRes;
 
@@ -107,7 +109,6 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
 
   boolean seqNameItalics;
 
-
   NJTree currentTree = null;
 
   boolean scaleAboveWrapped = false;
@@ -321,17 +322,18 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
     {
       if (!alignment.isNucleotide())
       {
-        showConservation=Cache.getDefault("SHOW_CONSERVATION", true);
-        showQuality=Cache.getDefault("SHOW_QUALITY", true);
+        showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
+        showQuality = Cache.getDefault("SHOW_QUALITY", true);
         showGroupConservation = Cache.getDefault("SHOW_GROUP_CONSERVATION",
                 false);
-      } 
+      }
       showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM",
               true);
       showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false);
-      normaliseSequenceLogo = Cache.getDefault("NORMALISE_CONSENSUS_LOGO", false);
+      normaliseSequenceLogo = Cache.getDefault("NORMALISE_CONSENSUS_LOGO",
+              false);
       showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
-      showConsensus=Cache.getDefault("SHOW_IDENTITY", true);
+      showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
       consensus = new AlignmentAnnotation("Consensus", "PID",
               new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
       consensus.hasText = true;
@@ -651,7 +653,7 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
               Desktop.instance).removeMappings(alignment.getCodonFrames());
     }
     this.alignment = align;
-    if (alignment!=null && alignment.getCodonFrames() != null)
+    if (alignment != null && alignment.getCodonFrames() != null)
     {
       StructureSelectionManager.getStructureSelectionManager(
               Desktop.instance).addMappings(alignment.getCodonFrames());
@@ -913,7 +915,6 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
     scaleRightWrapped = b;
   }
 
-
   public void setDataset(boolean b)
   {
     isDataset = b;
@@ -924,8 +925,6 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
     return isDataset;
   }
 
-
-
   public boolean getShowHiddenMarkers()
   {
     return showHiddenMarkers;
@@ -1052,11 +1051,11 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
     {
       sequenceColours = new Hashtable();
     }
-    for (SequenceGroup sg:alignment.getGroups())
+    for (SequenceGroup sg : alignment.getGroups())
     {
       if (sg.idColour != null)
       {
-        for (SequenceI s:sg.getSequences(getHiddenRepSequences()))
+        for (SequenceI s : sg.getSequences(getHiddenRepSequences()))
         {
           sequenceColours.put(s, sg.idColour);
         }
@@ -1274,7 +1273,6 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
     return seqvectors.toArray(new SequenceI[seqvectors.size()][]);
   }
 
-  
   public boolean isNormaliseSequenceLogo()
   {
     return normaliseSequenceLogo;
@@ -1285,30 +1283,32 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
     normaliseSequenceLogo = state;
   }
 
-
   /**
    * 
-   * @return true if alignment characters should be displayed 
+   * @return true if alignment characters should be displayed
    */
   public boolean isValidCharWidth()
   {
     return validCharWidth;
   }
-  private Hashtable<String, AutoCalcSetting> calcIdParams=new Hashtable<String, AutoCalcSetting>();
+
+  private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<String, AutoCalcSetting>();
+
   public AutoCalcSetting getCalcIdSettingsFor(String calcId)
   {
     return calcIdParams.get(calcId);
   }
 
-  public void setCalcIdSettingsFor(String calcId, AutoCalcSetting settings, boolean needsUpdate)
+  public void setCalcIdSettingsFor(String calcId, AutoCalcSetting settings,
+          boolean needsUpdate)
   {
     calcIdParams.put(calcId, settings);
-    // TODO: create a restart list to trigger any calculations that need to be restarted after load
+    // TODO: create a restart list to trigger any calculations that need to be
+    // restarted after load
     // calculator.getRegisteredWorkersOfClass(settings.getWorkerClass())
     if (needsUpdate)
     {
-      Cache.log.debug("trigger update for "+calcId);
+      Cache.log.debug("trigger update for " + calcId);
     }
   }
-  
 }