JAL-1385 expose core view model methods in interface

[jalview.git] / src / jalview / viewmodel / AlignmentViewport.java

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index f37e2bd..dc352f4 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -1,18 +1,18 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- *
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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
+ * 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
+ *  
+ * 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.viewmodel;
@@ -402,7 +402,8 @@ public abstract class AlignmentViewport implements AlignViewportI
     if (autoCalculateStrucConsensus && strucConsensus == null
             && alignment.isNucleotide() && alignment.hasRNAStructure())
     {
-
+      // secondary structure has been added - so init the consensus line
+      initRNAStructure();
     }
 
     // see note in mantis : issue number 8585
@@ -593,6 +594,7 @@ public abstract class AlignmentViewport implements AlignViewportI
    * 
    * @return null or the currently selected sequence region
    */
+  @Override
   public SequenceGroup getSelectionGroup()
   {
     return selectionGroup;
@@ -605,6 +607,7 @@ public abstract class AlignmentViewport implements AlignViewportI
    *          - group holding references to sequences in this alignment view
    * 
    */
+  @Override
   public void setSelectionGroup(SequenceGroup sg)
   {
     selectionGroup = sg;
@@ -1053,6 +1056,7 @@ public abstract class AlignmentViewport implements AlignViewportI
    * 
    * @return array of references to sequence objects
    */
+  @Override
   public SequenceI[] getSequenceSelection()
   {
     SequenceI[] sequences = null;
@@ -1075,6 +1079,7 @@ public abstract class AlignmentViewport implements AlignViewportI
    * 
    * @return String[]
    */
+  @Override
   public jalview.datamodel.CigarArray getViewAsCigars(
           boolean selectedRegionOnly)
   {
@@ -1091,6 +1096,7 @@ public abstract class AlignmentViewport implements AlignViewportI
    *          boolean true to just return the selected view
    * @return AlignmentView
    */
+  @Override
   public jalview.datamodel.AlignmentView getAlignmentView(
           boolean selectedOnly)
   {
@@ -1109,6 +1115,7 @@ public abstract class AlignmentViewport implements AlignViewportI
    *          is true)
    * @return AlignmentView
    */
+  @Override
   public jalview.datamodel.AlignmentView getAlignmentView(
           boolean selectedOnly, boolean markGroups)
   {
@@ -1124,6 +1131,7 @@ public abstract class AlignmentViewport implements AlignViewportI
    * 
    * @return String[]
    */
+  @Override
   public String[] getViewAsString(boolean selectedRegionOnly)
   {
     String[] selection = null;
@@ -1318,62 +1326,80 @@ public abstract class AlignmentViewport implements AlignViewportI
     {
       if (!alignment.isNucleotide())
       {
-        if (showConservation)
-        {
-          if (conservation == null)
-          {
-            conservation = new AlignmentAnnotation("Conservation",
-                    "Conservation of total alignment less than "
-                            + getConsPercGaps() + "% gaps",
-                    new Annotation[1], 0f, 11f,
-                    AlignmentAnnotation.BAR_GRAPH);
-            conservation.hasText = true;
-            conservation.autoCalculated = true;
-            alignment.addAnnotation(conservation);
-          }
-        }
-        if (showQuality)
-        {
-          if (quality == null)
-          {
-            quality = new AlignmentAnnotation("Quality",
-                    "Alignment Quality based on Blosum62 scores",
-                    new Annotation[1], 0f, 11f,
-                    AlignmentAnnotation.BAR_GRAPH);
-            quality.hasText = true;
-            quality.autoCalculated = true;
-            alignment.addAnnotation(quality);
-          }
-        }
+        initConservation();
+        initQuality();
       }
       else
       {
-        if (alignment.hasRNAStructure())
-        {
-          strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID",
-                  new Annotation[1], 0f, 100f,
-                  AlignmentAnnotation.BAR_GRAPH);
-          strucConsensus.hasText = true;
-          strucConsensus.autoCalculated = true;
-        }
+        initRNAStructure();
       }
+      initConsensus();
+    }
+  }
 
-      consensus = new AlignmentAnnotation("Consensus", "PID",
-              new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
-      consensus.hasText = true;
-      consensus.autoCalculated = true;
+  private void initConsensus()
+  {
 
-      if (showConsensus)
+    consensus = new AlignmentAnnotation("Consensus", "PID",
+            new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
+    consensus.hasText = true;
+    consensus.autoCalculated = true;
+
+    if (showConsensus)
+    {
+      alignment.addAnnotation(consensus);
+    }
+  }
+
+  private void initConservation()
+  {
+    if (showConservation)
+    {
+      if (conservation == null)
       {
-        alignment.addAnnotation(consensus);
-        if (strucConsensus != null)
-        {
-          alignment.addAnnotation(strucConsensus);
-        }
+        conservation = new AlignmentAnnotation("Conservation",
+                "Conservation of total alignment less than "
+                        + getConsPercGaps() + "% gaps",
+                new Annotation[1], 0f, 11f,
+                AlignmentAnnotation.BAR_GRAPH);
+        conservation.hasText = true;
+        conservation.autoCalculated = true;
+        alignment.addAnnotation(conservation);
       }
     }
   }
+  private void initQuality()
+  {
+    if (showQuality)
+    {
+      if (quality == null)
+      {
+        quality = new AlignmentAnnotation("Quality",
+                "Alignment Quality based on Blosum62 scores",
+                new Annotation[1], 0f, 11f,
+                AlignmentAnnotation.BAR_GRAPH);
+        quality.hasText = true;
+        quality.autoCalculated = true;
+        alignment.addAnnotation(quality);
+      }
+    }
+  }
+  private void initRNAStructure()
+  {
+    if (alignment.hasRNAStructure() && strucConsensus==null)
+    {
+      strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID",
+              new Annotation[1], 0f, 100f,
+              AlignmentAnnotation.BAR_GRAPH);
+      strucConsensus.hasText = true;
+      strucConsensus.autoCalculated = true;
 
+      if (showConsensus)
+      {
+        alignment.addAnnotation(strucConsensus);
+      }
+    }
+  }
   /*
    * (non-Javadoc)
    *