Case shifter

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

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 2e0c1cb..36b0a31 100755 (executable)
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -36,6 +36,9 @@ public class AlignViewport
   int startSeq;\r
   int endSeq;\r
 \r
+\r
+  boolean cursorMode = false;\r
+\r
   boolean showJVSuffix = true;\r
   boolean showText = true;\r
   boolean showColourText = false;\r
@@ -73,11 +76,18 @@ public class AlignViewport
   boolean scaleLeftWrapped = true;\r
   boolean scaleRightWrapped = true;\r
 \r
+  // The following vector holds the features which are\r
+ // currently visible, in the correct order or rendering\r
+  Hashtable featuresDisplayed = null;\r
+\r
+\r
   public Vector vconsensus;\r
   AlignmentAnnotation consensus;\r
   AlignmentAnnotation conservation;\r
   AlignmentAnnotation quality;\r
 \r
+  boolean autocalculateConsensus = true;\r
+\r
   public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!\r
 \r
   private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(this);\r
@@ -146,6 +156,11 @@ public class AlignViewport
     showSequenceFeatures = b;\r
   }\r
 \r
+  public boolean getShowSequenceFeatures()\r
+  {\r
+    return showSequenceFeatures;\r
+  }\r
+\r
 \r
   public void updateConservation()\r
   {\r
@@ -221,7 +236,7 @@ public class AlignViewport
                                              annotations,\r
                                              0f, // cons.qualityRange[0].floatValue(),\r
                                              11f, // cons.qualityRange[1].floatValue()\r
-                                             1);\r
+                                             AlignmentAnnotation.BAR_GRAPH);\r
       if (showConservation)\r
       {\r
         alignment.addAnnotation(conservation);\r
@@ -231,7 +246,7 @@ public class AlignViewport
                                         qannotations,\r
                                         cons.qualityRange[0].floatValue(),\r
                                         cons.qualityRange[1].floatValue(),\r
-                                        1);\r
+                                        AlignmentAnnotation.BAR_GRAPH);\r
       if (showQuality)\r
       {\r
         alignment.addAnnotation(quality);\r
@@ -294,7 +309,7 @@ public class AlignViewport
     if (consensus == null)\r
     {\r
       consensus = new AlignmentAnnotation("Consensus",\r
-                                          "PID", annotations, 0f, 100f, 1);\r
+                                          "PID", annotations, 0f, 100f, AlignmentAnnotation.BAR_GRAPH);\r
       if (showConsensus)\r
       {\r
         alignment.addAnnotation(consensus);\r