Update overview if features updated

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 2922f09..088d427 100755 (executable)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -43,7 +43,7 @@ public class AlignViewport
     int endRes;\r
     int startSeq;\r
     int endSeq;\r
-    boolean showFullId = false;\r
+    boolean showJVSuffix = true;\r
     boolean showText = true;\r
     boolean showColourText = false;\r
     boolean showBoxes = true;\r
@@ -86,6 +86,17 @@ public class AlignViewport
 \r
     boolean ignoreGapsInConsensusCalculation = false;\r
 \r
+    boolean isDataset = false;\r
+\r
+    boolean antiAlias = false;\r
+\r
+\r
+    public AlignViewport(AlignmentI al, boolean dataset)\r
+    {\r
+      isDataset = dataset;\r
+      setAlignment(al);\r
+      init();\r
+    }\r
     /**\r
      * Creates a new AlignViewport object.\r
      *\r
@@ -94,20 +105,19 @@ public class AlignViewport
     public AlignViewport(AlignmentI al)\r
     {\r
         setAlignment(al);\r
+        init();\r
+    }\r
+\r
+    void init()\r
+    {\r
         this.startRes = 0;\r
-        this.endRes = al.getWidth() - 1;\r
+        this.endRes = alignment.getWidth() - 1;\r
         this.startSeq = 0;\r
-        this.endSeq = al.getHeight() - 1;\r
+        this.endSeq = alignment.getHeight() - 1;\r
 \r
-        updateFromPreferences();\r
-    }\r
+      antiAlias = Cache.getDefault("ANTI_ALIAS", false);\r
 \r
-    /**\r
-     * DOCUMENT ME!\r
-     */\r
-    public void updateFromPreferences()\r
-    {\r
-      showFullId = Cache.getDefault("SHOW_FULL_ID", true);\r
+      showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);\r
       showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);\r
       showConservation = Cache.getDefault("SHOW_CONSERVATION", true);\r
 \r
@@ -137,9 +147,11 @@ public class AlignViewport
 \r
         // We must set conservation and consensus before setting colour,\r
         // as Blosum and Clustal require this to be done\r
-        updateConservation();\r
-\r
-        updateConsensus();\r
+        if(vconsensus==null && !isDataset)\r
+        {\r
+          updateConservation();\r
+          updateConsensus();\r
+        }\r
 \r
         if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)\r
         {\r
@@ -256,7 +268,7 @@ public class AlignViewport
                                                  ConsPercGaps + "% gaps",\r
                                                  annotations, 0f, // cons.qualityRange[0].floatValue(),\r
                                                  11f, // cons.qualityRange[1].floatValue()\r
-                                                 1);\r
+                                                 AlignmentAnnotation.BAR_GRAPH);\r
 \r
           if (showConservation)\r
           {\r
@@ -268,7 +280,7 @@ public class AlignViewport
                                             qannotations,\r
                                             cons.qualityRange[0].floatValue(),\r
                                             cons.qualityRange[1].floatValue(),\r
-                                            1);\r
+                                            AlignmentAnnotation.BAR_GRAPH);\r
 \r
           if (showQuality)\r
           {\r
@@ -352,7 +364,7 @@ public class AlignViewport
         if (consensus == null)\r
         {\r
           consensus = new AlignmentAnnotation("Consensus", "PID",\r
-                                              annotations, 0f, 100f, 1);\r
+                                              annotations, 0f, 100f,AlignmentAnnotation.BAR_GRAPH);\r
 \r
           if (showIdentity)\r
           {\r
@@ -914,9 +926,9 @@ public class AlignViewport
      *\r
      * @return DOCUMENT ME!\r
      */\r
-    public boolean getShowFullId()\r
+    public boolean getShowJVSuffix()\r
     {\r
-        return showFullId;\r
+        return showJVSuffix;\r
     }\r
 \r
     /**\r
@@ -924,11 +936,12 @@ public class AlignViewport
      *\r
      * @param b DOCUMENT ME!\r
      */\r
-    public void setShowFullId(boolean b)\r
+    public void setShowJVSuffix(boolean b)\r
     {\r
-        showFullId = b;\r
+        showJVSuffix = b;\r
     }\r
 \r
+\r
     /**\r
      * DOCUMENT ME!\r
      *\r
@@ -1058,4 +1071,14 @@ public class AlignViewport
     {\r
      return ignoreGapsInConsensusCalculation;\r
     }\r
+\r
+    public void setDataset(boolean b)\r
+    {\r
+      isDataset = b;\r
+    }\r
+\r
+    public boolean isDataset()\r
+    {\r
+      return isDataset;\r
+    }\r
 }\r