Feature settings

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

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 40d3dd4..bef5e1a 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
@@ -57,8 +57,7 @@ public class AlignViewport
 \r
   int charHeight;\r
   int charWidth;\r
-  int chunkWidth;\r
-  int chunkHeight;\r
+  int wrappedWidth;\r
 \r
   Font font = new Font("SansSerif", Font.PLAIN, 10);\r
   AlignmentI alignment;\r
@@ -74,6 +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
@@ -99,7 +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
@@ -147,9 +151,17 @@ public class AlignViewport
     showSequenceFeatures = b;\r
   }\r
 \r
+  public boolean getShowSequenceFeatures()\r
+  {\r
+    return showSequenceFeatures;\r
+  }\r
+\r
 \r
   public void updateConservation()\r
   {\r
+    if(alignment.isNucleotide())\r
+          return;\r
+\r
     Conservation cons = new jalview.analysis.Conservation("All",\r
         jalview.schemes.ResidueProperties.propHash, 3,\r
         alignment.getSequences(), 0,\r
@@ -219,7 +231,7 @@ 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
@@ -229,7 +241,7 @@ 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
@@ -292,7 +304,7 @@ 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
@@ -440,24 +452,14 @@ public class AlignViewport
     return charHeight;\r
   }\r
 \r
-  public void setChunkWidth(int w)\r
-  {\r
-    this.chunkWidth = w;\r
-  }\r
-\r
-  public int getChunkWidth()\r
-  {\r
-    return chunkWidth;\r
-  }\r
-\r
-  public void setChunkHeight(int h)\r
+  public void setWrappedWidth(int w)\r
   {\r
-    this.chunkHeight = h;\r
+    this.wrappedWidth = w;\r
   }\r
 \r
-  public int getChunkHeight()\r
+  public int getwrappedWidth()\r
   {\r
-    return chunkHeight;\r
+    return wrappedWidth;\r
   }\r
 \r
   public AlignmentI getAlignment()\r
@@ -604,14 +606,14 @@ 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