X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fproject%2FJalview2XML.java;h=186f7866b2e7fdbe3652af5660ab2f7815789a67;hb=cb51e62fe2166b236ef488e0a8f35081fcd71388;hp=1a2527087e4fc13bc101c8a15f2fc1b7c852f1b9;hpb=72fb6df14f1ff426bbafa18dcc9a90450da93018;p=jalview.git

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index 1a25270..186f786 100644
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -150,6 +150,7 @@ import jalview.xml.binding.jalview.ThresholdType;
 import jalview.xml.binding.jalview.VAMSAS;
 
 import java.awt.Color;
+import java.awt.Dimension;
 import java.awt.Font;
 import java.awt.Rectangle;
 import java.io.BufferedReader;
@@ -4997,23 +4998,23 @@ public class Jalview2XML
   }
 
   AlignFrame loadViewport(String file, List<JSeq> JSEQ,
-          List<SequenceI> hiddenSeqs, AlignmentI al,
-          JalviewModel jm, Viewport view, String uniqueSeqSetId,
-          String viewId, List<JvAnnotRow> autoAlan)
+          List<SequenceI> hiddenSeqs, AlignmentI al, JalviewModel jm,
+          Viewport view, String uniqueSeqSetId, String viewId,
+          List<JvAnnotRow> autoAlan)
   {
     AlignFrame af = null;
     af = new AlignFrame(al, safeInt(view.getWidth()),
             safeInt(view.getHeight()), uniqueSeqSetId, viewId)
-//    {
-//    	
-//    	@Override
-//    	protected void processKeyEvent(java.awt.event.KeyEvent e) {
-//    		System.out.println("Jalview2XML   AF " + e);
-//    		super.processKeyEvent(e);
-//    		
-//    	}
-//    	
-//    }
+    // {
+    //
+    // @Override
+    // protected void processKeyEvent(java.awt.event.KeyEvent e) {
+    // System.out.println("Jalview2XML AF " + e);
+    // super.processKeyEvent(e);
+    //
+    // }
+    //
+    // }
     ;
     af.alignPanel.setHoldRepaint(true);
     af.setFileName(file, FileFormat.Jalview);
@@ -5091,9 +5092,8 @@ public class Jalview2XML
 
     viewport.setColourText(safeBoolean(view.isShowColourText()));
 
-    viewport
-            .setConservationSelected(
-                    safeBoolean(view.isConservationSelected()));
+    viewport.setConservationSelected(
+            safeBoolean(view.isConservationSelected()));
     viewport.setIncrement(safeInt(view.getConsThreshold()));
     viewport.setShowJVSuffix(safeBoolean(view.isShowFullId()));
     viewport.setRightAlignIds(safeBoolean(view.isRightAlignIds()));
@@ -5179,9 +5179,8 @@ public class Jalview2XML
     af.changeColour(cs);
     viewport.setColourAppliesToAllGroups(true);
 
-    viewport
-            .setShowSequenceFeatures(
-                    safeBoolean(view.isShowSequenceFeatures()));
+    viewport.setShowSequenceFeatures(
+            safeBoolean(view.isShowSequenceFeatures()));
 
     viewport.setCentreColumnLabels(view.isCentreColumnLabels());
     viewport.setIgnoreGapsConsensus(view.isIgnoreGapsinConsensus(), null);
@@ -5202,13 +5201,13 @@ public class Jalview2XML
               .getFeatureRenderer();
       FeaturesDisplayed fdi;
       viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
-      String[] renderOrder = new String[jm.getFeatureSettings()
-              .getSetting().size()];
+      String[] renderOrder = new String[jm.getFeatureSettings().getSetting()
+              .size()];
       Map<String, FeatureColourI> featureColours = new Hashtable<>();
       Map<String, Float> featureOrder = new Hashtable<>();
 
-      for (int fs = 0; fs < jm.getFeatureSettings()
-              .getSetting().size(); fs++)
+      for (int fs = 0; fs < jm.getFeatureSettings().getSetting()
+              .size(); fs++)
       {
         Setting setting = jm.getFeatureSettings().getSetting().get(fs);
         String featureType = setting.getType();
@@ -5220,8 +5219,8 @@ public class Jalview2XML
                 .getMatcherSet();
         if (filters != null)
         {
-          FeatureMatcherSetI filter = Jalview2XML
-                  .parseFilter(featureType, filters);
+          FeatureMatcherSetI filter = Jalview2XML.parseFilter(featureType,
+                  filters);
           if (!filter.isEmpty())
           {
             fr.setFeatureFilter(featureType, filter);
@@ -5253,8 +5252,7 @@ public class Jalview2XML
           float max = setting.getMax() == null ? 1f
                   : setting.getMax().floatValue();
           FeatureColourI gc = new FeatureColour(maxColour, minColour,
-                  maxColour,
-                  noValueColour, min, max);
+                  maxColour, noValueColour, min, max);
           if (setting.getAttributeName().size() > 0)
           {
             gc.setAttributeName(setting.getAttributeName().toArray(
@@ -5288,8 +5286,7 @@ public class Jalview2XML
         }
         else
         {
-          featureColours.put(featureType,
-                  new FeatureColour(maxColour));
+          featureColours.put(featureType, new FeatureColour(maxColour));
         }
         renderOrder[fs] = featureType;
         if (setting.getOrder() != null)
@@ -5357,8 +5354,9 @@ public class Jalview2XML
     String complementaryViewId = view.getComplementId();
     if (complementaryViewId == null)
     {
-      Desktop.addInternalFrame(af, view.getTitle(),
+      Dimension dim = Platform.getDimIfEmbedded(af,
               safeInt(view.getWidth()), safeInt(view.getHeight()));
+      Desktop.addInternalFrame(af, view.getTitle(), dim.width, dim.height);
       // recompute any autoannotation
       af.alignPanel.updateAnnotation(false, true);
       reorderAutoannotation(af, al, autoAlan);
@@ -6118,14 +6116,7 @@ public class Jalview2XML
     AlignFrame af = loadFromObject(jm, null, false, null);
     af.getAlignPanels().clear();
     af.closeMenuItem_actionPerformed(true);
-
-    /*
-     * if(ap.av.getAlignment().getAlignmentAnnotation()!=null) { for(int i=0;
-     * i<ap.av.getAlignment().getAlignmentAnnotation().length; i++) {
-     * if(!ap.av.getAlignment().getAlignmentAnnotation()[i].autoCalculated) {
-     * af.alignPanel.av.getAlignment().getAlignmentAnnotation()[i] =
-     * ap.av.getAlignment().getAlignmentAnnotation()[i]; } } }
-     */
+    af.alignPanel.setHoldRepaint(false);
 
     return af.alignPanel;
   }
@@ -6476,8 +6467,10 @@ public class Jalview2XML
                   axis.getXPos(), axis.getYPos(), axis.getZPos());
         }
 
+        Dimension dim = Platform.getDimIfEmbedded(panel, 475, 450);
         Desktop.addInternalFrame(panel, MessageManager.formatMessage(
-                "label.calc_title", "PCA", modelName), 475, 450);
+                "label.calc_title", "PCA", modelName), dim.width,
+                dim.height);
       }
     } catch (Exception ex)
     {