X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Forg%2Fvamsas%2Ftest%2Fsimpleclient%2FArchiveWriter.java;h=d6f8ee941b0bf2d12172858c82eb416208e1d8b0;hb=7700d838b129db99edacb208b3153546795a33c7;hp=91b1d9e21fe2f5ee98f5f461d631d9aaa3c878c7;hpb=4fc6d93d0c1a33ab5e0765b87d9263baa1798318;p=vamsas.git diff --git a/src/org/vamsas/test/simpleclient/ArchiveWriter.java b/src/org/vamsas/test/simpleclient/ArchiveWriter.java index 91b1d9e..d6f8ee9 100644 --- a/src/org/vamsas/test/simpleclient/ArchiveWriter.java +++ b/src/org/vamsas/test/simpleclient/ArchiveWriter.java @@ -13,8 +13,10 @@ import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.vamsas.client.simpleclient.VamsasArchive; import org.vamsas.client.simpleclient.VamsasArchiveReader; +import org.vamsas.objects.core.Alignment; import org.vamsas.objects.core.ApplicationData; import org.vamsas.objects.core.Entry; +import org.vamsas.objects.core.Instance; import org.vamsas.objects.core.Provenance; import org.vamsas.objects.core.VAMSAS; import org.vamsas.objects.core.VamsasDocument; @@ -27,7 +29,7 @@ public class ArchiveWriter { * form is ArchiveWriter new/modified argive command list */ - static Log log = LogFactory.getLog("org.vamsas.test.simpleclient.ArchiveWriter"); + static Log log = LogFactory.getLog(ArchiveWriter.class); private static void mergeVecs(Object[] destvec, Object[] svec1, Object[] svec2) { int i; @@ -38,15 +40,16 @@ public class ArchiveWriter { } // Merge appDataReferences require transfer of jar entries, perhaps with a renaming of the entry. // Merge appDatas require eventually unique URNS + // TODO: merging global appdata from different documents where same app has written them causes conflict - public static Hashtable hashOfAppDatas(Hashtable ht, ApplicationData[] appdatas) { + public static Hashtable hashOfAppDatas(Hashtable ht, Instance[] appdatas) { if (ht==null) ht = new Hashtable(); for (int i=0, j=appdatas.length; i0) { @@ -142,7 +145,7 @@ public class ArchiveWriter { VamsasArchive varc = new VamsasArchive(newarch, true); VamsasDocument docroot; docroot = new VamsasDocument(); - docroot.setProvenance(ProvenanceStuff.newProvenance("ArchiveWriter", "Created new Vamsas Document")); + docroot.setProvenance(ProvenanceStuff.newProvenance("ArchiveWriter", "user", "Created new Vamsas Document")); while (++argpos