Submissions for secondary structure prediction are now filtered to remove empty seque...

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index f57e993..7f86753 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
@@ -86,10 +86,15 @@ public class AlignViewport
 \r
     boolean ignoreGapsInConsensusCalculation = false;\r
 \r
-    boolean showTranslation = false;\r
-\r
     boolean isDataset = 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
@@ -98,13 +103,17 @@ 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
-\r
+        this.endSeq = alignment.getHeight() - 1;\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
@@ -134,7 +143,7 @@ public class AlignViewport
 \r
         // We must set conservation and consensus before setting colour,\r
         // as Blosum and Clustal require this to be done\r
-        if(vconsensus==null)\r
+        if(vconsensus==null && !isDataset)\r
         {\r
           updateConservation();\r
           updateConsensus();\r
@@ -913,9 +922,9 @@ 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
@@ -923,11 +932,12 @@ 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
@@ -1058,16 +1068,6 @@ public class AlignViewport
      return ignoreGapsInConsensusCalculation;\r
     }\r
 \r
-    public void showTranslation(boolean b)\r
-    {\r
-      this.showTranslation = b;\r
-    }\r
-\r
-    public boolean getShowTranslation()\r
-    {\r
-      return showTranslation;\r
-    }\r
-\r
     public void setDataset(boolean b)\r
     {\r
       isDataset = b;\r