JAL-2163 set title for the alignframe from restored view state

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

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index c0e1ebe..0f15505 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -108,6 +108,7 @@ import java.lang.reflect.InvocationTargetException;
 import java.net.MalformedURLException;
 import java.net.URL;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Enumeration;
 import java.util.HashMap;
 import java.util.HashSet;
@@ -165,6 +166,8 @@ public class Jalview2XML
    */
   Map<String, SequenceI> seqRefIds = null;
 
+  Map<String, SequenceI> incompleteSeqs = null;
+
   List<SeqFref> frefedSequence = null;
 
   boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
@@ -220,6 +223,10 @@ public class Jalview2XML
       {
         seqsToIds.clear();
       }
+      if (incompleteSeqs != null)
+      {
+        incompleteSeqs.clear();
+      }
       // seqRefIds = null;
       // seqsToIds = null;
     }
@@ -242,6 +249,10 @@ public class Jalview2XML
     {
       seqRefIds = new HashMap<String, SequenceI>();
     }
+    if (incompleteSeqs == null)
+    {
+      incompleteSeqs = new HashMap<String, SequenceI>();
+    }
     if (frefedSequence == null)
     {
       frefedSequence = new ArrayList<SeqFref>();
@@ -386,13 +397,32 @@ public class Jalview2XML
     }
     if (unresolved>0)
     {
-      System.err.println("There were "+unresolved+" forward references left unresolved on the stack.");
+      System.err.println("Jalview Project Import: There were " + unresolved
+              + " forward references left unresolved on the stack.");
     }
     if (failedtoresolve>0)
     {
       System.err.println("SERIOUS! " + failedtoresolve
               + " resolvable forward references failed to resolve.");
     }
+    if (incompleteSeqs != null && incompleteSeqs.size() > 0)
+    {
+      System.err.println("Jalview Project Import: There are "
+              + incompleteSeqs.size()
+              + " sequences which may have incomplete metadata.");
+      if (incompleteSeqs.size() < 10)
+      {
+        for (SequenceI s : incompleteSeqs.values())
+        {
+          System.err.println(s.toString());
+        }
+      }
+      else
+      {
+        System.err
+                .println("Too many to report. Skipping output of incomplete sequences.");
+      }
+    }
   }
 
   /**
@@ -463,7 +493,20 @@ public class Jalview2XML
     {
       return;
     }
+    saveAllFrames(Arrays.asList(frames), jout);
+  }
 
+  /**
+   * core method for storing state for a set of AlignFrames.
+   * 
+   * @param frames
+   *          - frames involving all data to be exported (including containing
+   *          splitframes)
+   * @param jout
+   *          - project output stream
+   */
+  private void saveAllFrames(List<AlignFrame> frames, JarOutputStream jout)
+  {
     Hashtable<String, AlignFrame> dsses = new Hashtable<String, AlignFrame>();
 
     /*
@@ -483,9 +526,9 @@ public class Jalview2XML
       List<String> viewIds = new ArrayList<String>();
 
       // REVERSE ORDER
-      for (int i = frames.length - 1; i > -1; i--)
+      for (int i = frames.size() - 1; i > -1; i--)
       {
-        AlignFrame af = frames[i];
+        AlignFrame af = frames.get(i);
         // skip ?
         if (skipList != null
                 && skipList
@@ -588,30 +631,20 @@ public class Jalview2XML
   {
     try
     {
-      int ap = 0;
-      int apSize = af.alignPanels.size();
       FileOutputStream fos = new FileOutputStream(jarFile);
       JarOutputStream jout = new JarOutputStream(fos);
-      Hashtable<String, AlignFrame> dsses = new Hashtable<String, AlignFrame>();
-      List<String> viewIds = new ArrayList<String>();
+      List<AlignFrame> frames = new ArrayList<AlignFrame>();
 
-      for (AlignmentPanel apanel : af.alignPanels)
+      // resolve splitframes
+      if (af.getViewport().getCodingComplement() != null)
       {
-        String jfileName = apSize == 1 ? fileName : fileName + ap;
-        ap++;
-        if (!jfileName.endsWith(".xml"))
-        {
-          jfileName = jfileName + ".xml";
-        }
-        saveState(apanel, jfileName, jout, viewIds);
-        String dssid = getDatasetIdRef(af.getViewport().getAlignment()
-                .getDataset());
-        if (!dsses.containsKey(dssid))
-        {
-          dsses.put(dssid, af);
-        }
+        frames = ((SplitFrame) af.getSplitViewContainer()).getAlignFrames();
+      }
+      else
+      {
+        frames.add(af);
       }
-      writeDatasetFor(dsses, fileName, jout);
+      saveAllFrames(frames, jout);
       try
       {
         jout.flush();
@@ -2743,6 +2776,18 @@ public class Jalview2XML
       SequenceI tmpSeq = seqRefIds.get(seqId);
       if (tmpSeq != null)
       {
+        if (!incompleteSeqs.containsKey(seqId))
+        {
+          // may not need this check, but keep it for at least 2.9,1 release
+          if (tmpSeq.getStart()!=jseqs[i].getStart() || tmpSeq.getEnd()!=jseqs[i].getEnd())
+          { 
+            System.err
+                    .println("Warning JAL-2154 regression: updating start/end for sequence "
+                    + tmpSeq.toString());
+          }
+        } else {
+          incompleteSeqs.remove(seqId);
+        }
         tmpSeq.setStart(jseqs[i].getStart());
         tmpSeq.setEnd(jseqs[i].getEnd());
         tmpseqs.add(tmpSeq);
@@ -4494,7 +4539,7 @@ public class Jalview2XML
       }
     }
     af.setMenusFromViewport(af.viewport);
-
+    af.setTitle(view.getTitle());
     // TODO: we don't need to do this if the viewport is aready visible.
     /*
      * Add the AlignFrame to the desktop (it may be 'gathered' later), unless it
@@ -5103,6 +5148,7 @@ public class Jalview2XML
           djs.setEnd(jmap.getMap().getToHighest());
           djs.setVamsasId(uniqueSetSuffix + sqid);
           jmap.setTo(djs);
+          incompleteSeqs.put(sqid, djs);
           seqRefIds.put(sqid, djs);
 
         }