added description of alignment quality scores and separated

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

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 209f939..8c6c7d2 100755 (executable)
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -36,7 +36,7 @@ public class AlignViewport
   int startSeq;\r
   int endSeq;\r
 \r
-  boolean showFullId = true;\r
+  boolean showJVSuffix = true;\r
   boolean showText = true;\r
   boolean showColourText = false;\r
   boolean showBoxes = true;\r
@@ -73,6 +73,11 @@ 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
@@ -98,7 +103,7 @@ public class AlignViewport
       String param = applet.getParameter("showFullId");\r
       if (param != null)\r
       {\r
-        showFullId = Boolean.valueOf(param).booleanValue();\r
+        showJVSuffix = Boolean.valueOf(param).booleanValue();\r
       }\r
 \r
       param = applet.getParameter("showAnnotation");\r
@@ -221,7 +226,7 @@ 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 +236,7 @@ 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 +299,7 @@ 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
@@ -596,14 +601,14 @@ public class AlignViewport
     return colourAppliesToAllGroups;\r
   }\r
 \r
-  public boolean getShowFullId()\r
+  public boolean getShowJVSuffix()\r
   {\r
-    return showFullId;\r
+    return showJVSuffix;\r
   }\r
 \r
-  public void setShowFullId(boolean b)\r
+  public void setShowJVSuffix(boolean b)\r
   {\r
-    showFullId = b;\r
+    showJVSuffix = b;\r
   }\r
 \r
   public boolean getShowAnnotation()\r