Use sequence description

[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 d8dfe62..a036988 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
@@ -267,7 +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
@@ -293,7 +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
@@ -334,41 +336,21 @@ 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
-        af.colourTextMenuItem.setSelected(view.getShowColourText());\r
         af.viewport.setConservationSelected(view.getConservationSelected());\r
-        af.conservationMenuItem.setSelected(view.getConservationSelected());\r
-\r
         af.viewport.setShowJVSuffix(view.getShowFullId());\r
-        af.seqLimits.setSelected(view.getShowFullId());\r
-\r
         af.viewport.setFont(new java.awt.Font(view.getFontName(),\r
                 view.getFontStyle(), view.getFontSize()));\r
         af.alignPanel.fontChanged();\r
 \r
         af.viewport.setRenderGaps(view.getRenderGaps());\r
-        af.renderGapsMenuItem.setSelected(view.getRenderGaps());\r
-\r
         af.viewport.setWrapAlignment(view.getWrapAlignment());\r
-        af.wrapMenuItem.setSelected(view.getWrapAlignment());\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
         af.viewport.setShowText(view.getShowText());\r
-        af.viewTextMenuItem.setSelected(view.getShowText());\r
 \r
         ColourSchemeI cs = null;\r
 \r
@@ -386,11 +368,10 @@ 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
-        af.setColourSelected(view.getBgColour());\r
         af.viewport.setGlobalColourScheme(cs);\r
         af.viewport.setColourAppliesToAllGroups(false);\r
         af.changeColour(cs);\r
@@ -400,12 +381,8 @@ public class Jalview2XML_V1
         }\r
 \r
         af.viewport.setColourAppliesToAllGroups(true);\r
+        af.viewport.showSequenceFeatures = view.getShowSequenceFeatures();\r
 \r
-        if (view.getShowSequenceFeatures())\r
-        {\r
-           af.viewport.showSequenceFeatures = true;\r
-           af.showSeqFeatures.setSelected(true);\r
-        }\r
 \r
         if(jms.getFeatureSettings()!=null)\r
         {\r
@@ -427,6 +404,7 @@ public class Jalview2XML_V1
          af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;\r
         }\r
 \r
+        af.setMenusFromViewport(af.viewport);\r
 \r
         Desktop.addInternalFrame(af, view.getTitle(),\r
              view.getWidth(), view.getHeight());\r