showqual, showcons never used

[jalview.git] / src / jalview / gui / Jalview2XML_V1.java

diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java
index d84b8db..1d52819 100755 (executable)
--- a/src/jalview/gui/Jalview2XML_V1.java
+++ b/src/jalview/gui/Jalview2XML_V1.java
@@ -1,6 +1,6 @@
 /*\r
  * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
  *\r
  * This program is free software; you can redistribute it and/or\r
  * modify it under the terms of the GNU General Public License\r
@@ -113,10 +113,8 @@ public class Jalview2XML_V1
                 for (int i = 0; i < entryCount; i++)\r
                 {\r
                     jarentry = jin.getNextJarEntry();\r
-\r
                   }\r
 \r
-\r
                   class NoDescIDResolver implements IDResolver\r
                   {\r
                     public Object resolve(String idref)\r
@@ -269,7 +267,7 @@ public class Jalview2XML_V1
         Viewport[] views = jms.getViewport();\r
         Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER\r
 \r
-        AlignFrame af = new AlignFrame(al);\r
+        AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight());\r
 \r
 \r
         //  af.changeColour() );\r
@@ -295,7 +293,9 @@ public class Jalview2XML_V1
                                 groups[i].getColour());\r
                     }\r
 \r
-                    cs.setThreshold(groups[i].getPidThreshold(), true);\r
+                    if(cs!=null)\r
+                      cs.setThreshold(groups[i].getPidThreshold(), true);\r
+\r
                 }\r
 \r
                 Vector seqs = new Vector();\r
@@ -318,7 +318,7 @@ public class Jalview2XML_V1
                 if (groups[i].getConsThreshold() != 0)\r
                 {\r
                     jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",\r
-                            ResidueProperties.propHash, 3, sg.sequences, 0,\r
+                            ResidueProperties.propHash, 3, sg.getSequences(false), 0,\r
                             sg.getWidth() - 1);\r
                     c.calculate();\r
                     c.verdict(false, 25);\r
@@ -336,9 +336,6 @@ public class Jalview2XML_V1
         af.viewport.setStartRes(view.getStartRes());\r
         af.viewport.setStartSeq(view.getStartSeq());\r
         af.viewport.setShowAnnotation(view.getShowAnnotation());\r
-        af.viewport.showConservation = view.getShowConservation();\r
-        af.viewport.showQuality = view.getShowQuality();\r
-        af.viewport.showIdentity = view.getShowIdentity();\r
         af.viewport.setAbovePIDThreshold(view.getPidSelected());\r
         af.abovePIDThreshold.setSelected(view.getPidSelected());\r
         af.viewport.setColourText(view.getShowColourText());\r
@@ -359,16 +356,13 @@ public class Jalview2XML_V1
         af.viewport.setWrapAlignment(view.getWrapAlignment());\r
         af.wrapMenuItem.setSelected(view.getWrapAlignment());\r
 \r
-        if (view.getWrapAlignment())\r
-        {\r
-            af.alignPanel.setWrapAlignment(view.getWrapAlignment());\r
-        }\r
-        else\r
-        {\r
-            af.annotationPanelMenuItem.setState(view.getShowAnnotation());\r
-            af.viewport.setShowAnnotation(view.getShowAnnotation());\r
-            af.alignPanel.setAnnotationVisible(view.getShowAnnotation());\r
-        }\r
+\r
+        af.alignPanel.setWrapAlignment(view.getWrapAlignment());\r
+\r
+        af.annotationPanelMenuItem.setState(view.getShowAnnotation());\r
+        af.viewport.setShowAnnotation(view.getShowAnnotation());\r
+        af.alignPanel.setAnnotationVisible(view.getShowAnnotation());\r
+\r
 \r
         af.viewport.setShowBoxes(view.getShowBoxes());\r
         af.viewBoxesMenuItem.setSelected(view.getShowBoxes());\r
@@ -391,7 +385,7 @@ public class Jalview2XML_V1
             if(cs!=null)\r
             {\r
               cs.setThreshold(view.getPidThreshold(), true);\r
-              cs.setConsensus(af.viewport.vconsensus);\r
+              cs.setConsensus(af.viewport.hconsensus);\r
             }\r
         }\r
 \r