X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fpacked%2FParsePackedSet.java;h=01369b9014a8915334093d9f686cd67e6f1f76c6;hb=ed87c8b39a1b48ef6bdf013106d8a667d559c4be;hp=20b2061e33b80fa565f2d4537c76969e3c5180cf;hpb=2ddb613232cf825e989a5b0e7772f83a09dd682e;p=jalview.git

diff --git a/src/jalview/io/packed/ParsePackedSet.java b/src/jalview/io/packed/ParsePackedSet.java
index 20b2061..01369b9 100644
--- a/src/jalview/io/packed/ParsePackedSet.java
+++ b/src/jalview/io/packed/ParsePackedSet.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * 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 
+ * 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 
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.io.packed;
 
 import jalview.datamodel.AlignmentI;
@@ -8,8 +28,9 @@ import jalview.io.IdentifyFile;
 import jalview.io.packed.DataProvider.JvDataType;
 
 import java.io.BufferedReader;
+import java.io.IOException;
 import java.util.ArrayList;
-import java.util.Hashtable;
+import java.util.HashMap;
 import java.util.List;
 
 public class ParsePackedSet
@@ -45,7 +66,7 @@ public class ParsePackedSet
         String fmt = null;
         try
         {
-          fmt = new IdentifyFile().Identify(src, false);
+          fmt = new IdentifyFile().identify(src, false);
         } catch (Exception ex)
         {
           exerror = ex;
@@ -76,6 +97,7 @@ public class ParsePackedSet
               // deuniquify and construct/merge additional dataset entries if
               // necessary.
               context.addAlignment(al);
+              context.updateSetModified(true);
               rslt.add(al);
               deuniquify = true;
             }
@@ -101,8 +123,16 @@ public class ParsePackedSet
           {
             br = new BufferedReader(src.getReader());
           }
-          new jalview.io.AnnotationFile().parseAnnotationFrom(
-                  context.getLastAlignment(), br);
+          // TODO: add columnSelection to context
+          if (new jalview.io.AnnotationFile().parseAnnotationFrom(
+                  context.getLastAlignment(), null, br))
+          {
+            context.updateSetModified(true);
+          }
+          else
+          {
+            errmsg = "Annotation file contained no data.";
+          }
 
         } catch (Exception e)
         {
@@ -123,16 +153,17 @@ public class ParsePackedSet
       }
       if (dta.getType().equals(JvDataType.FEATURES))
       {
-        // check the context has a place to store feature rendering definitions, if not, create one.
-        if (context.featureColours==null)
+        // check the context has a place to store feature rendering definitions,
+        // if not, create one.
+        if (context.featureColours == null)
         {
-          context.featureColours = new Hashtable();
+          context.featureColours = new HashMap<String, Object>();
         }
         try
         {
           jalview.io.FeaturesFile ff = new jalview.io.FeaturesFile(src);
-          ff.parse(context.getLastAlignment(), context.featureColours,
-                  false);
+          context.updateSetModified(ff.parse(context.getLastAlignment(),
+                  context.featureColours, false, context.relaxedIdMatching));
         } catch (Exception e)
         {
           errmsg = ("Failed to parse the Features file associated with the alignment.");
@@ -155,6 +186,7 @@ public class ParsePackedSet
 
             context.addTreeFromFile(nf);
             rslt.add(nf);
+            context.updateSetModified(true);
           }
         } catch (Exception e)
         {
@@ -163,7 +195,24 @@ public class ParsePackedSet
         }
 
       }
-
+      if (exerror != null)
+      {
+        if (errmsg != null && errmsg.length() > 0)
+        {
+          throw new IOException(errmsg, exerror);
+        }
+        else
+        {
+          throw new IOException(errmsg, exerror);
+        }
+      }
+      else
+      {
+        if (errmsg != null && errmsg.length() > 0)
+        {
+          throw new IOException(errmsg);
+        }
+      }
     }
     if (deuniquify)
     {
@@ -249,5 +298,13 @@ public class ParsePackedSet
       // import with deuniquify info, and compare results to input.
 
     }
+    else
+    {
+      if (context.getLastAlignmentSet().isModified())
+      {
+        System.err
+                .println("Initial alignment set was modified and any associated views should be updated.");
+      }
+    }
   }
 }