X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fpacked%2FParsePackedSet.java;h=91575bfd7403b6674a1f7b5ac65e7673d0cb613d;hb=2305d687bac5ed8a76ecb93c54c7b090a928e362;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..91575bf 100644
--- a/src/jalview/io/packed/ParsePackedSet.java
+++ b/src/jalview/io/packed/ParsePackedSet.java
@@ -1,16 +1,40 @@
+/*
+ * 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.api.FeatureColourI;
 import jalview.datamodel.AlignmentI;
 import jalview.io.AppletFormatAdapter;
+import jalview.io.FileFormatI;
 import jalview.io.FileParse;
 import jalview.io.FormatAdapter;
 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;
+import java.util.Locale;
 
 public class ParsePackedSet
 {
@@ -42,10 +66,10 @@ public class ParsePackedSet
       FileParse src = dta.getDataSource();
       if (dta.getType().equals(DataProvider.JvDataType.ALIGNMENT))
       {
-        String fmt = null;
+        FileFormatI fmt = null;
         try
         {
-          fmt = new IdentifyFile().Identify(src, false);
+          fmt = new IdentifyFile().identify(src, false);
         } catch (Exception ex)
         {
           exerror = ex;
@@ -54,31 +78,24 @@ public class ParsePackedSet
 
         if (fmt != null)
         {
-          if (!FormatAdapter.isValidIOFormat(fmt, false))
+          // parse the alignment
+          AlignmentI al = null;
+          try
           {
-            errmsg = fmt;
-            exerror = null;
+            al = new FormatAdapter().readFromFile(src, fmt);
+          } catch (Exception e)
+          {
+            errmsg = "Failed to parse alignment from result set";
+            exerror = e;
           }
-          else
+          if (al != null)
           {
-            // parse the alignment
-            AlignmentI al = null;
-            try
-            {
-              al = new FormatAdapter().readFromFile(src, fmt);
-            } catch (Exception e)
-            {
-              errmsg = "Failed to parse alignment from result set";
-              exerror = e;
-            }
-            if (al != null)
-            {
-              // deuniquify and construct/merge additional dataset entries if
-              // necessary.
-              context.addAlignment(al);
-              rslt.add(al);
-              deuniquify = true;
-            }
+            // deuniquify and construct/merge additional dataset entries if
+            // necessary.
+            context.addAlignment(al);
+            context.updateSetModified(true);
+            rslt.add(al);
+            deuniquify = true;
           }
         }
       }
@@ -101,8 +118,16 @@ 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 +148,18 @@ 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, FeatureColourI>();
         }
         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 +182,7 @@ public class ParsePackedSet
 
             context.addTreeFromFile(nf);
             rslt.add(nf);
+            context.updateSetModified(true);
           }
         } catch (Exception e)
         {
@@ -163,7 +191,24 @@ 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)
     {
@@ -189,8 +234,8 @@ public class ParsePackedSet
     {
       String type = args[i++];
       final String file = args[i++];
-      final JvDataType jtype = DataProvider.JvDataType.valueOf(type
-              .toUpperCase());
+      final JvDataType jtype = DataProvider.JvDataType
+              .valueOf(type.toUpperCase(Locale.ROOT));
       if (jtype != null)
       {
         final FileParse fp;
@@ -209,7 +254,7 @@ public class ParsePackedSet
       else
       {
         System.out.println("Couldn't parse source type token '"
-                + type.toUpperCase() + "'");
+                + type.toUpperCase(Locale.ROOT) + "'");
       }
     }
     if (i < args.length)
@@ -228,8 +273,8 @@ public class ParsePackedSet
     ParsePackedSet pps;
     try
     {
-      newdm = (pps = new ParsePackedSet()).getAlignment(
-              context = new JalviewDataset(), dp);
+      newdm = (pps = new ParsePackedSet())
+              .getAlignment(context = new JalviewDataset(), dp);
     } catch (Exception e)
     {
       System.out.println("Test failed for these arguments.\n");
@@ -249,5 +294,13 @@ 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.");
+      }
+    }
   }
 }