X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FJalview2XML_V1.java;h=491746a47dbc169e3838d8e6cfc141636965ce39;hb=fe17c9998066fe039ba952c266c2445db5adfe82;hp=d8dfe62bbd5e06e9fbc9952b41e83770d46916e0;hpb=61505ac1511435b067e647f5c7c9050e5c1eef41;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java
index d8dfe62..491746a 100755
--- a/src/jalview/gui/Jalview2XML_V1.java
+++ b/src/jalview/gui/Jalview2XML_V1.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -132,7 +132,7 @@ public class Jalview2XML_V1
 
                     object = (JalviewModel) object.unmarshal(in);
 
-                    af = LoadFromObject(object);
+                    af = LoadFromObject(object, file);
                     entryCount++;
                 }
             }
@@ -164,7 +164,7 @@ public class Jalview2XML_V1
         return af;
     }
 
-    AlignFrame LoadFromObject(JalviewModel object)
+    AlignFrame LoadFromObject(JalviewModel object, String file)
     {
         Vector seqids = new Vector();
         SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
@@ -182,7 +182,6 @@ public class Jalview2XML_V1
                     vamsasSeq[i].getSequence());
             jseqs[i].setStart(JSEQ[i].getStart());
             jseqs[i].setEnd(JSEQ[i].getEnd());
-            jseqs[i].setColor(new java.awt.Color(JSEQ[i].getColour()));
             seqids.add(jseqs[i]);
         }
 
@@ -267,7 +266,18 @@ public class Jalview2XML_V1
         Viewport[] views = jms.getViewport();
         Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
 
-        AlignFrame af = new AlignFrame(al);
+        AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight());
+
+        af.setFileName(file, "Jalview");
+
+        for (int i = 0; i < JSEQ.length; i++)
+        {
+          af.viewport.setSequenceColour(
+              af.viewport.alignment.getSequenceAt(i),
+              new java.awt.Color(
+                  JSEQ[i].getColour()));
+        }
+
 
 
         //  af.changeColour() );
@@ -293,7 +303,9 @@ public class Jalview2XML_V1
                                 groups[i].getColour());
                     }
 
-                    cs.setThreshold(groups[i].getPidThreshold(), true);
+                    if(cs!=null)
+                      cs.setThreshold(groups[i].getPidThreshold(), true);
+
                 }
 
                 Vector seqs = new Vector();
@@ -334,41 +346,21 @@ public class Jalview2XML_V1
         af.viewport.setStartRes(view.getStartRes());
         af.viewport.setStartSeq(view.getStartSeq());
         af.viewport.setShowAnnotation(view.getShowAnnotation());
-        af.viewport.showConservation = view.getShowConservation();
-        af.viewport.showQuality = view.getShowQuality();
-        af.viewport.showIdentity = view.getShowIdentity();
         af.viewport.setAbovePIDThreshold(view.getPidSelected());
-        af.abovePIDThreshold.setSelected(view.getPidSelected());
         af.viewport.setColourText(view.getShowColourText());
-        af.colourTextMenuItem.setSelected(view.getShowColourText());
         af.viewport.setConservationSelected(view.getConservationSelected());
-        af.conservationMenuItem.setSelected(view.getConservationSelected());
-
         af.viewport.setShowJVSuffix(view.getShowFullId());
-        af.seqLimits.setSelected(view.getShowFullId());
-
         af.viewport.setFont(new java.awt.Font(view.getFontName(),
                 view.getFontStyle(), view.getFontSize()));
         af.alignPanel.fontChanged();
 
         af.viewport.setRenderGaps(view.getRenderGaps());
-        af.renderGapsMenuItem.setSelected(view.getRenderGaps());
-
         af.viewport.setWrapAlignment(view.getWrapAlignment());
-        af.wrapMenuItem.setSelected(view.getWrapAlignment());
-
-
         af.alignPanel.setWrapAlignment(view.getWrapAlignment());
-
-        af.annotationPanelMenuItem.setState(view.getShowAnnotation());
         af.viewport.setShowAnnotation(view.getShowAnnotation());
         af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
-
-
         af.viewport.setShowBoxes(view.getShowBoxes());
-        af.viewBoxesMenuItem.setSelected(view.getShowBoxes());
         af.viewport.setShowText(view.getShowText());
-        af.viewTextMenuItem.setSelected(view.getShowText());
 
         ColourSchemeI cs = null;
 
@@ -386,11 +378,10 @@ public class Jalview2XML_V1
             if(cs!=null)
             {
               cs.setThreshold(view.getPidThreshold(), true);
-              cs.setConsensus(af.viewport.vconsensus);
+              cs.setConsensus(af.viewport.hconsensus);
             }
         }
 
-        af.setColourSelected(view.getBgColour());
         af.viewport.setGlobalColourScheme(cs);
         af.viewport.setColourAppliesToAllGroups(false);
         af.changeColour(cs);
@@ -400,12 +391,8 @@ public class Jalview2XML_V1
         }
 
         af.viewport.setColourAppliesToAllGroups(true);
+        af.viewport.showSequenceFeatures = view.getShowSequenceFeatures();
 
-        if (view.getShowSequenceFeatures())
-        {
-           af.viewport.showSequenceFeatures = true;
-           af.showSeqFeatures.setSelected(true);
-        }
 
         if(jms.getFeatureSettings()!=null)
         {
@@ -427,6 +414,7 @@ public class Jalview2XML_V1
          af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
         }
 
+        af.setMenusFromViewport(af.viewport);
 
         Desktop.addInternalFrame(af, view.getTitle(),
              view.getWidth(), view.getHeight());