X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=41dd71dcfe16126e760f780f3a8a7a1f26041793;hb=02783b1d0f22e82e7854777646e39df0fc77de74;hp=8872be09fd169defbed5299f37bea00a64570e00;hpb=6d981e3a3cac0e7f487d2b3d40e45cfd6ca8435c;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 8872be0..41dd71d 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1,18 +1,18 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * 
  * This file is part of Jalview.
- *
+ * 
  * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
+ * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.gui;
@@ -38,9 +38,9 @@ import jalview.schemabinding.version2.*;
 import jalview.schemes.*;
 import jalview.util.Platform;
 import jalview.util.jarInputStreamProvider;
-import jalview.ws.jws2.AAConsClient;
+import jalview.ws.jws2.AAConClient;
 import jalview.ws.jws2.Jws2Discoverer;
-import jalview.ws.jws2.dm.AAConsSettings;
+import jalview.ws.jws2.dm.AAConSettings;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
 import jalview.ws.params.ArgumentI;
 import jalview.ws.params.AutoCalcSetting;
@@ -48,11 +48,11 @@ import jalview.ws.params.WsParamSetI;
 
 /**
  * Write out the current jalview desktop state as a Jalview XML stream.
- *
+ * 
  * Note: the vamsas objects referred to here are primitive versions of the
  * VAMSAS project schema elements - they are not the same and most likely never
  * will be :)
- *
+ * 
  * @author $author$
  * @version $Revision: 1.134 $
  */
@@ -60,7 +60,7 @@ public class Jalview2XML
 {
   /**
    * create/return unique hash string for sq
-   *
+   * 
    * @param sq
    * @return new or existing unique string for sq
    */
@@ -266,7 +266,7 @@ public class Jalview2XML
 
   /**
    * Writes a jalview project archive to the given Jar output stream.
-   *
+   * 
    * @param jout
    */
   public void SaveState(JarOutputStream jout)
@@ -407,7 +407,7 @@ public class Jalview2XML
   /**
    * create a JalviewModel from an algnment view and marshall it to a
    * JarOutputStream
-   *
+   * 
    * @param ap
    *          panel to create jalview model for
    * @param fileName
@@ -464,7 +464,7 @@ public class Jalview2XML
     }
 
     JSeq jseq;
-    Set<String> calcIdSet=new HashSet<String>();
+    Set<String> calcIdSet = new HashSet<String>();
 
     // SAVE SEQUENCES
     String id = "";
@@ -1004,6 +1004,7 @@ public class Jalview2XML
         groups[i].setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus());
         groups[i].setShowConsensusHistogram(sg.isShowConsensusHistogram());
         groups[i].setShowSequenceLogo(sg.isShowSequenceLogo());
+        groups[i].setNormaliseSequenceLogo(sg.isNormaliseSequenceLogo());
         for (int s = 0; s < sg.getSize(); s++)
         {
           jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg
@@ -1117,6 +1118,7 @@ public class Jalview2XML
     view.setTextColThreshold(av.thresholdTextColour);
     view.setShowConsensusHistogram(av.isShowConsensusHistogram());
     view.setShowSequenceLogo(av.isShowSequenceLogo());
+    view.setNormaliseSequenceLogo(av.isNormaliseSequenceLogo());
     view.setShowGroupConsensus(av.isShowGroupConsensus());
     view.setShowGroupConservation(av.isShowGroupConservation());
     view.setShowNPfeatureTooltip(av.isShowNpFeats());
@@ -1354,7 +1356,7 @@ public class Jalview2XML
                   .getPreset(calcIdParam.getName());
           if (parmSet != null)
           {
-            // TODO : check we have a good match with settings in AACons -
+            // TODO : check we have a good match with settings in AACon -
             // otherwise we'll need to create a new preset
           }
         }
@@ -1363,7 +1365,7 @@ public class Jalview2XML
           argList = parmSet.getArguments();
           parmSet = null;
         }
-        AAConsSettings settings = new AAConsSettings(
+        AAConSettings settings = new AAConSettings(
                 calcIdParam.isAutoUpdate(), service, parmSet, argList);
         av.setCalcIdSettingsFor(calcIdParam.getCalcId(), settings,
                 calcIdParam.isNeedsUpdate());
@@ -1668,6 +1670,8 @@ public class Jalview2XML
 
     try
     {
+      // create list to store references for any new Jmol viewers created
+      newStructureViewers=new Vector<AppJmol>();
       // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
       // Workaround is to make sure caller implements the JarInputStreamProvider
       // interface
@@ -1675,6 +1679,7 @@ public class Jalview2XML
 
       jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
       af = LoadJalviewAlign(jprovider);
+      setLoadingFinishedForNewStructureViewers();
     } catch (MalformedURLException e)
     {
       errorMessage = "Invalid URL format for '" + file + "'";
@@ -2267,16 +2272,19 @@ public class Jalview2XML
         // Construct new annotation from model.
         AnnotationElement[] ae = an[i].getAnnotationElement();
         jalview.datamodel.Annotation[] anot = null;
-
+        java.awt.Color firstColour = null;
+        int anpos;
         if (!an[i].getScoreOnly())
         {
           anot = new jalview.datamodel.Annotation[al.getWidth()];
           for (int aa = 0; aa < ae.length && aa < anot.length; aa++)
           {
-            if (ae[aa].getPosition() >= anot.length)
+            anpos = ae[aa].getPosition();
+
+            if (anpos >= anot.length)
               continue;
 
-            anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
+            anot[anpos] = new jalview.datamodel.Annotation(
 
             ae[aa].getDisplayCharacter(), ae[aa].getDescription(),
                     (ae[aa].getSecondaryStructure() == null || ae[aa]
@@ -2292,8 +2300,11 @@ public class Jalview2XML
             // {
             // anot[ae[aa].getPosition()].displayCharacter = "";
             // }
-            anot[ae[aa].getPosition()].colour = new java.awt.Color(
-                    ae[aa].getColour());
+            anot[anpos].colour = new java.awt.Color(ae[aa].getColour());
+            if (firstColour == null)
+            {
+              firstColour = anot[anpos].colour;
+            }
           }
         }
         jalview.datamodel.AlignmentAnnotation jaa = null;
@@ -2309,7 +2320,7 @@ public class Jalview2XML
                   an[i].getGraphType());
 
           jaa.graphGroup = an[i].getGraphGroup();
-
+          jaa._linecolour = firstColour;
           if (an[i].getThresholdLine() != null)
           {
             jaa.setThreshold(new jalview.datamodel.GraphLine(an[i]
@@ -2329,6 +2340,7 @@ public class Jalview2XML
         {
           jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
                   an[i].getDescription(), anot);
+          jaa._linecolour = firstColour;
         }
         // register new annotation
         if (an[i].getId() != null)
@@ -2472,6 +2484,10 @@ public class Jalview2XML
         {
           sg.setshowSequenceLogo(groups[i].isShowSequenceLogo());
         }
+        if (groups[i].hasNormaliseSequenceLogo())
+        {
+          sg.setNormaliseSequenceLogo(groups[i].isNormaliseSequenceLogo());
+        }
         if (groups[i].hasIgnoreGapsinConsensus())
         {
           sg.setIgnoreGapsConsensus(groups[i].getIgnoreGapsinConsensus());
@@ -2956,6 +2972,7 @@ public class Jalview2XML
                       sview = new AppJmol(pdbf, id, sq, alf.alignPanel,
                               useinJmolsuperpos, usetoColourbyseq,
                               jmolColouring, fileloc, rect, vid);
+                      addNewStructureViewer(sview);
                     } catch (OutOfMemoryError ex)
                     {
                       new OOMWarning("restoring structure view for PDB id "
@@ -3025,6 +3042,27 @@ public class Jalview2XML
     // and finally return.
     return af;
   }
+  Vector<AppJmol> newStructureViewers=null;
+  protected void addNewStructureViewer(AppJmol sview)
+  {
+    if (newStructureViewers!=null)
+    {
+      sview.jmb.setFinishedLoadingFromArchive(false);
+      newStructureViewers.add(sview);
+    }
+  }
+  protected void setLoadingFinishedForNewStructureViewers()
+  {
+    if (newStructureViewers!=null)
+    {
+      for (AppJmol sview:newStructureViewers)
+      {
+        sview.jmb.setFinishedLoadingFromArchive(true);
+      }
+      newStructureViewers.clear();
+      newStructureViewers=null;
+    }
+  }
 
   AlignFrame loadViewport(String file, JSeq[] JSEQ, Vector hiddenSeqs,
           Alignment al, JalviewModelSequence jms, Viewport view,
@@ -3289,6 +3327,10 @@ public class Jalview2XML
     {
       af.viewport.setShowSequenceLogo(false);
     }
+    if (view.hasNormaliseSequenceLogo())
+    {
+      af.viewport.setNormaliseSequenceLogo(view.getNormaliseSequenceLogo());
+    }
     if (view.hasShowDbRefTooltip())
     {
       af.viewport.setShowDbRefs(view.getShowDbRefTooltip());
@@ -3409,7 +3451,7 @@ public class Jalview2XML
     // TODO: we don't need to do this if the viewport is aready visible.
     Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
             view.getHeight());
-    af.alignPanel.updateAnnotation(false); // recompute any autoannotation
+    af.alignPanel.updateAnnotation(false, true); // recompute any autoannotation
     reorderAutoannotation(af, al, autoAlan);
     return af;
   }
@@ -3517,7 +3559,7 @@ public class Jalview2XML
 
   /**
    * TODO remove this method
-   *
+   * 
    * @param view
    * @return AlignFrame bound to sequenceSetId from view, if one exists. private
    *         AlignFrame getSkippedFrame(Viewport view) { if (skipList==null) {
@@ -3528,7 +3570,7 @@ public class Jalview2XML
 
   /**
    * Check if the Jalview view contained in object should be skipped or not.
-   *
+   * 
    * @param object
    * @return true if view's sequenceSetId is a key in skipList
    */
@@ -3601,7 +3643,7 @@ public class Jalview2XML
   }
 
   /**
-   *
+   * 
    * @param vamsasSeq
    *          sequence definition to create/merge dataset sequence for
    * @param ds
@@ -3725,7 +3767,7 @@ public class Jalview2XML
 
   /**
    * make a new dataset ID for this jalview dataset alignment
-   *
+   * 
    * @param dataset
    * @return
    */
@@ -3912,7 +3954,7 @@ public class Jalview2XML
 
   /*
    * (non-Javadoc)
-   *
+   * 
    * @see java.lang.Object#finalize()
    */
   @Override
@@ -3990,13 +4032,13 @@ public class Jalview2XML
    * finalize and clearSeqRefs will not clear the tables when the Jalview2XML
    * object goes out of scope. - also populates the datasetIds hashtable with
    * alignment objects containing dataset sequences
-   *
+   * 
    * @param vobj2jv
    *          Map from ID strings to jalview datamodel
    * @param jv2vobj
    *          Map from jalview datamodel to ID strings
-   *
-   *
+   * 
+   * 
    */
   public void setObjectMappingTables(Hashtable vobj2jv,
           IdentityHashMap jv2vobj)
@@ -4068,7 +4110,7 @@ public class Jalview2XML
    * set the uniqueSetSuffix used to prefix/suffix object IDs for jalview
    * objects created from the project archive. If string is null (default for
    * construction) then suffix will be set automatically.
-   *
+   * 
    * @param string
    */
   public void setUniqueSetSuffix(String string)
@@ -4080,7 +4122,7 @@ public class Jalview2XML
   /**
    * uses skipList2 as the skipList for skipping views on sequence sets
    * associated with keys in the skipList
-   *
+   * 
    * @param skipList2
    */
   public void setSkipList(Hashtable skipList2)