Annotations move when full alignment edited

[jalview.git] / src / jalview / gui / Jalview2XML.java

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 6e3bffe..0cac9c1 100755 (executable)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -21,8 +21,6 @@ package jalview.gui;
 
 import jalview.schemes.*;
 
-import jalview.gui.*;
-
 import java.io.*;
 
 import java.net.*;
@@ -58,6 +56,8 @@ public class Jalview2XML
    */
   Hashtable viewportsAdded;
 
+  Hashtable annotationIds = new Hashtable();
+
   String uniqueSetSuffix = "";
 
 
@@ -142,7 +142,7 @@ public class Jalview2XML
     }
 
     // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
-    public void SaveAlignment(AlignFrame af, String jarFile,
+    public boolean SaveAlignment(AlignFrame af, String jarFile,
         String fileName)
     {
         try
@@ -163,10 +163,12 @@ public class Jalview2XML
 
           out.close();
           jout.close();
+          return true;
         }
         catch (Exception ex)
         {
           ex.printStackTrace();
+          return false;
         }
     }
 
@@ -230,7 +232,7 @@ public class Jalview2XML
               vamsasSeq = new Sequence();
               vamsasSeq.setId(id + "");
               vamsasSeq.setName(jds.getName());
-              vamsasSeq.setSequence(jds.getSequence());
+              vamsasSeq.setSequence(jds.getSequenceAsString());
               vamsasSeq.setDescription(jds.getDescription());
 
               if (jds.getDatasetSequence().getDBRef() != null)
@@ -263,16 +265,20 @@ public class Jalview2XML
             {
               jseq.setHidden(av.alignment.getHiddenSequences().isHidden(jds));
 
-              if(jal.getSequenceAt(i).getHiddenSequences()!=null)
+              if(av.hiddenRepSequences!=null
+              && av.hiddenRepSequences.containsKey(jal.getSequenceAt(i)))
               {
-                jalview.datamodel.SequenceI [] reps =
-                    jal.getSequenceAt(i).getHiddenSequences().getSequencesInOrder(jal);
+                jalview.datamodel.SequenceI[] reps =
+                    ( (jalview.datamodel.SequenceGroup)
+                     av.hiddenRepSequences.get(
+                         jal.getSequenceAt(i))).getSequencesInOrder(jal);
 
                 for(int h=0; h<reps.length; h++)
                 {
-                  jseq.addHiddenSequences(
-                      jal.findIndex(reps[h])
-                      );
+                  if (reps[h] != jal.getSequenceAt(i))
+                    jseq.addHiddenSequences(
+                        jal.findIndex(reps[h])
+                        );
                 }
               }
             }
@@ -335,19 +341,20 @@ public class Jalview2XML
                 pdb.setId(entry.getId());
                 pdb.setType(entry.getType());
 
+
                 if(entry.getFile()!=null)
                 {
+                  pdb.setFile(entry.getFile());
                   if(pdbfiles==null)
                     pdbfiles = new Vector();
 
-
                   if(!pdbfiles.contains(entry.getId()))
                   {
                     pdbfiles.addElement(entry.getId());
                     try
                     {
                       File file = new File(entry.getFile());
-                      if(file.exists())
+                      if(file.exists() && jout!=null)
                       {
                         byte[] data = new byte[ (int) file.length()];
                         jout.putNextEntry(new JarEntry(entry.getId()));
@@ -449,6 +456,13 @@ public class Jalview2XML
             {
                 Annotation an = new Annotation();
 
+                if(aa[i].annotationId!=null)
+                {
+                  annotationIds.put(aa[i].annotationId, aa[i]);
+                }
+
+                an.setId(aa[i].annotationId);
+
                 if (aa[i].label.equals("Quality") ||
                         aa[i].label.equals("Conservation") ||
                         aa[i].label.equals("Consensus"))
@@ -573,7 +587,7 @@ public class Jalview2XML
                 groups[i].setTextCol2(sg.textColour2.getRGB());
                 groups[i].setTextColThreshold(sg.thresholdTextColour);
 
-                for (int s = 0; s < sg.getSize(false); s++)
+                for (int s = 0; s < sg.getSize(); s++)
                 {
                     jalview.datamodel.Sequence seq =
                         (jalview.datamodel.Sequence) sg.getSequenceAt(s);
@@ -669,7 +683,7 @@ public class Jalview2XML
         view.setShowBoxes(av.getShowBoxes());
         view.setShowColourText(av.getColourText());
         view.setShowFullId(av.getShowJVSuffix());
-        view.setRightAlignIds(av.idsAlignRight);
+        view.setRightAlignIds(av.rightAlignIds);
         view.setShowSequenceFeatures(av.showSequenceFeatures);
         view.setShowText(av.getShowText());
         view.setWrapAlignment(av.getWrapAlignment());
@@ -952,6 +966,7 @@ public class Jalview2XML
             System.out.println("Successfully loaded archive file");
             return af;
           }
+          ex.printStackTrace();
 
             System.err.println("Exception whilst loading jalview XML file : " +
                 ex + "\n");
@@ -981,6 +996,7 @@ public class Jalview2XML
 
     String loadPDBFile(String file, String pdbId)
     {
+      System.out.println(file +" "+pdbId);
       try
       {
         JarInputStream jin = null;
@@ -1199,10 +1215,20 @@ public class Jalview2XML
                  continue;
                }
 
+               if (an[i].getId() != null
+                   && annotationIds.containsKey(an[i].getId()))
+               {
+                 al.addAnnotation(
+                     (jalview.datamodel.AlignmentAnnotation)annotationIds.get(an[i].getId())
+                     );
+
+                 continue;
+              }
+
                 AnnotationElement[] ae = an[i].getAnnotationElement();
                 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al.getWidth()];
 
-                for (int aa = 0; aa < ae.length; aa++)
+                for (int aa = 0; aa < ae.length && aa<anot.length; aa++)
                 {
                     anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].getDisplayCharacter(),
                             ae[aa].getDescription(),
@@ -1238,6 +1264,12 @@ public class Jalview2XML
                             an[i].getDescription(), anot);
                 }
 
+                if(an[i].getId()!=null)
+                {
+                  annotationIds.put(an[i].getId(), jaa);
+                  jaa.annotationId = an[i].getId();
+                }
+
                 if(an[i].getSequenceRef()!=null)
                 {
                   jaa.createSequenceMapping(
@@ -1299,7 +1331,7 @@ public class Jalview2XML
                 if (groups[i].getConsThreshold() != 0)
                 {
                     jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",
-                            ResidueProperties.propHash, 3, sg.getSequences(false), 0,
+                            ResidueProperties.propHash, 3, sg.getSequences(null), 0,
                             sg.getWidth() - 1);
                     c.calculate();
                     c.verdict(false, 25);
@@ -1360,12 +1392,17 @@ public class Jalview2XML
         {
           for(int s=0; s<JSEQ.length; s++)
           {
+            jalview.datamodel.SequenceGroup hidden =
+                new jalview.datamodel.SequenceGroup();
+
             for(int r=0; r<JSEQ[s].getHiddenSequencesCount(); r++)
             {
-              al.getSequenceAt(s).addHiddenSequence(
-                  al.getSequenceAt( JSEQ[s].getHiddenSequences(r)  )
+              hidden.addSequence(
+                  al.getSequenceAt(JSEQ[s].getHiddenSequences(r))
+                  , false
                   );
             }
+            af.viewport.hideRepSequences(al.getSequenceAt(s), hidden);
           }
 
           jalview.datamodel.SequenceI [] hseqs = new
@@ -1403,11 +1440,14 @@ public class Jalview2XML
           af.alignPanel.adjustAnnotationHeight();
         }
 
-        af.viewport.viewName = view.getViewName();
+        if(view.getViewName()!=null)
+        {
+          af.viewport.viewName = view.getViewName();
+          af.setInitialTabVisible();
+        }
         af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
             view.getHeight());
-        af.viewport.setStartRes(view.getStartRes());
-        af.viewport.setStartSeq(view.getStartSeq());
+
         af.viewport.setShowAnnotation(view.getShowAnnotation());
         af.viewport.setAbovePIDThreshold(view.getPidSelected());
 
@@ -1415,7 +1455,7 @@ public class Jalview2XML
 
         af.viewport.setConservationSelected(view.getConservationSelected());
         af.viewport.setShowJVSuffix(view.getShowFullId());
-        af.viewport.idsAlignRight=view.getRightAlignIds();
+        af.viewport.rightAlignIds=view.getRightAlignIds();
         af.viewport.setFont(new java.awt.Font(view.getFontName(),
                 view.getFontStyle(), view.getFontSize()));
         af.alignPanel.fontChanged();
@@ -1433,6 +1473,8 @@ public class Jalview2XML
         af.viewport.textColour2 = new java.awt.Color(view.getTextCol2());
         af.viewport.thresholdTextColour = view.getTextColThreshold();
 
+        af.viewport.setStartRes(view.getStartRes());
+        af.viewport.setStartSeq(view.getStartSeq());
 
         ColourSchemeI cs = null;
 
@@ -1669,6 +1711,18 @@ public class Jalview2XML
       af.alignPanels.clear();
       af.closeMenuItem_actionPerformed(true);
 
+    /*  if(ap.av.alignment.getAlignmentAnnotation()!=null)
+      {
+        for(int i=0; i<ap.av.alignment.getAlignmentAnnotation().length; i++)
+        {
+          if(!ap.av.alignment.getAlignmentAnnotation()[i].autoCalculated)
+          {
+            af.alignPanel.av.alignment.getAlignmentAnnotation()[i] =
+                ap.av.alignment.getAlignmentAnnotation()[i];
+          }
+        }
+      }   */
+
       return af.alignPanel;
     }
 }